DeepRetinotopy Toolbox

Author: Fernanda Ribeiro

Date: 12 Nov 2025

License:

MIT License

Note: If this notebook uses neuroimaging tools from Neurocontainers, those tools retain their original licenses. Please see Neurodesk citation guidelines for details.

Citation and Resources

Tools included in this workflow

deepretinotopy:

• Ribeiro, F. L. et al. (2025). Predicting functional topography of the human visual cortex from cortical anatomy at scale. bioRxiv

Dataset

NYU Retinotopy Dataset

Himmelberg, Marc M. and Kurzawski, Jan W. and Benson, Noah C. and Carrasco, Marisa and Winawer, Jonathan. “NYU Retinotopy dataset” 2021. doi:10.18112/openneuro.ds003787.v1.0.1

DeepRetinotopy toolbox

This interactive notebook demonstrates how to predict retinotopic maps from anatomical data using a geometric deep learning model of retinotopy. For more details about the toolbox, please check our repository. The accompanying manuscript will be available soon.

Requirements:

1. freesurfer directory;

2. HCP “fs_LR-deformed_to-fsaverage” surfaces, available here.

Load Software Tools

%%capture 
!pip install nilearn nibabel numpy

# we can use module to load deepretinotopy in a specific version
import module
import os
await module.load('deepretinotopy/1.0.18')
await module.list()

['deepretinotopy/1.0.18']

# Request a freesurfer license and store it in your homedirectory. This is just an example - please replace with your license id:
!echo "Steffen.Bollmann@cai.uq.edu.au" > ~/.license
!echo "21029" >> ~/.license
!echo "*Cqyn12sqTCxo" >> ~/.license
!echo "FSxgcvGkNR59Y" >> ~/.license

Download data

Let’s start by downloading some data available on OpenNeuro. DeepRetinotopy only requires a minimal subset of FreeSurfer outputs, which means you can significantly reduce storage requirements by downloading only the following files per subject:

Essential Files

<subject_id>/surf/
├── lh.white          # White matter surface
├── lh.pial           # Pial surface  
├── lh.sphere.reg     # Spherical surface for resampling
├── rh.white          # White matter surface
├── rh.pial           # Pial surface
└── rh.sphere.reg     # Spherical surface for resampling

Note: The toolbox automatically generates the midthickness surfaces and curvature data from these base files during processing. All other FreeSurfer outputs (thickness maps, parcellations, etc.) are not required for retinotopic mapping prediction.

!mkdir -p ./data

os.chdir('./data')
!datalad install https://github.com/OpenNeuroDatasets/ds003787.git # install NYU retinotopy dataset
os.chdir('ds003787/derivatives/freesurfer') # change directories
list_of_subs = os.listdir('.')

# download required files to run deepretinotopy
for sub in list_of_subs:
    for hemisphere in ['lh', 'rh']:
        for file in ['pial', 'white', 'sphere', 'sphere.reg', 'thickness']:
            cmd=f"""datalad get {sub}/surf/{hemisphere}.{file}""" 
            os.system(cmd)

Cloning:   0%|                             | 0.00/2.00 [00:00<?, ? candidates/s]
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Receiving:  14%|███                   | 19.1k/137k [00:00<00:00, 191k Objects/s]
Receiving:  36%|███████▉              | 49.2k/137k [00:00<00:00, 230k Objects/s]
Receiving:  54%|███████████▉          | 73.9k/137k [00:00<00:00, 237k Objects/s]
Receiving:  72%|███████████████▊      | 98.5k/137k [00:00<00:00, 230k Objects/s]
Receiving:  89%|████████████████████▍  | 122k/137k [00:00<00:00, 217k Objects/s]
                                                                                
Resolving:   0%|                              | 0.00/22.7k [00:00<?, ? Deltas/s]
Resolving:  27%|█████▋               | 6.13k/22.7k [00:00<00:00, 61.3k Deltas/s]
Resolving:  58%|████████████▏        | 13.2k/22.7k [00:00<00:00, 66.1k Deltas/s]
Resolving:  90%|██████████████████▉  | 20.4k/22.7k [00:00<00:00, 68.4k Deltas/s]
[INFO   ] Remote origin not usable by git-annex; setting annex-ignore           
[INFO   ] https://github.com/OpenNeuroDatasets/ds003787.git/config download failed: Not Found 
install(ok): /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787 (dataset)
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get(ok): derivatives/freesurfer/sub-wlsubj088/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj088/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj088/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj088/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj019/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj092/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj115/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj084/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj079/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj043/surf/rh.thickness (file) [from s3-PUBLIC...]

Since we have preprocessed data available, the only remaining requirements are the HCP template surfaces. Thus, we need to create a “templates” folder (for example, ./templates/) and download the following files from the link above:

• “fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii”;

• “fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii”;

# Set up paths relative to current directory
os.environ['PATH_FREESURFER_DIR'] = "."
os.environ['PATH_HCP_TEMPLATE_SURFACE'] = "../../templates"
os.environ['DATASET_NAME'] = "nyu"
os.environ['MAPS'] = "polarAngle,eccentricity"

# Create templates directory
os.makedirs(os.environ['PATH_HCP_TEMPLATE_SURFACE'], exist_ok=True)

# Download templates to the relative path
!cd $PATH_HCP_TEMPLATE_SURFACE && \
wget https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii && \
wget https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii

--2026-01-20 10:56:10--  https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii
Resolving github.com (github.com)... 140.82.121.4
Connecting to github.com (github.com)|140.82.121.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/Washington-University/HCPpipelines/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii [following]
--2026-01-20 10:56:10--  https://raw.githubusercontent.com/Washington-University/HCPpipelines/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.108.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 720487 (704K) [text/plain]
Saving to: ‘fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii’

fs_LR-deformed_to-f 100%[===================>] 703.60K  --.-KB/s    in 0.04s   

2026-01-20 10:56:10 (15.4 MB/s) - ‘fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii’ saved [720487/720487]

--2026-01-20 10:56:10--  https://github.com/Washington-University/HCPpipelines/raw/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii
Resolving github.com (github.com)... 140.82.121.4
Connecting to github.com (github.com)|140.82.121.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/Washington-University/HCPpipelines/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii [following]
--2026-01-20 10:56:11--  https://raw.githubusercontent.com/Washington-University/HCPpipelines/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.110.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 707932 (691K) [text/plain]
Saving to: ‘fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii’

fs_LR-deformed_to-f 100%[===================>] 691.34K  --.-KB/s    in 0.04s   

2026-01-20 10:56:11 (15.4 MB/s) - ‘fs_LR-deformed_to-fsaverage.R.sphere.32k_fs_LR.surf.gii’ saved [707932/707932]

Running deepRetinotopy for a single subject

Here, we illustrate how to run deepRetinotopy for a single subject. Note that, if no output directory is provided, all maps are saved within each subject subdirectory in the freesurfer directory.

## Process single subject without an explicit output directory
!deepRetinotopy -s $PATH_FREESURFER_DIR -t $PATH_HCP_TEMPLATE_SURFACE -d $DATASET_NAME -m $MAPS -i sub-wlsubj001

Processing single subject: sub-wlsubj001
Log files location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs
Output log: deepRetinotopy_20260120_105813_output.log
Error log: deepRetinotopy_20260120_105813_error.log
--------------------------------------------------------------------------------
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------------------------------------------------
Log files: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260120_105813_output.log and deepRetinotopy_20260120_105813_error.log
--------------------------------------------------------------------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-fsaverage template surfaces: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/templates
Dataset name: nyu
Maps: polarAngle eccentricity
Processing mode: Single subject (sub-wlsubj001)
Fast midthickness generation: yes
Output mode: In-place (within FreeSurfer directory structure)
Execution mode: Complete pipeline (Steps 1, 2, and 3)
--------------------------------------------------------------------------------
Processing left hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 1 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf
[sub-wlsubj001] Fast mode enabled.
[sub-wlsubj001] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj001] Converting surfaces...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.pial.gii as a surface
[sub-wlsubj001] Generating midthickness surface...
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.graymid.gii
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.graymid as a surface
[sub-wlsubj001] Computing curvature...
total integrated curvature = -2.905*4pi (-36.505) --> 4 handles
ICI = 155.2, FI = 1392.0, variation=22879.765
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.graymid.K...done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.graymid.H...done.
[sub-wlsubj001] Mid-thickness surface has been generated
[sub-wlsubj001] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj001] Running freesurfer-resample-prep...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.midthickness.surf.gii.temp32485.white.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.midthickness.surf.gii.temp32485.pial.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.sphere.reg.surf.gii as a surface
[sub-wlsubj001] Converting curvature data...
[sub-wlsubj001] Resampling native data to fsaverage space...
[sub-wlsubj001] Data resampling complete
=== Subject sub-wlsubj001 completed in 2 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 2m 11s
Subject processed: sub-wlsubj001
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_32655_f780bd54_406
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.31 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_LH_model.pt
Running inference for model 1...
Inference completed in 0.29 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Created output directory
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.53 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 50s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_32655_f780bd54_406
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the left hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the left hemisphere...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

[sub-wlsubj001] Transforming polar angle map of the left hemisphere...
[sub-wlsubj001] Applying mask to the predicted map of the left hemisphere...

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 5s
Subject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_32930_e5b9d32a_62045
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.29 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_LH_model.pt
Running inference for model 1...
Inference completed in 0.28 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.50 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 47s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_32930_e5b9d32a_62045
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the left hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the left hemisphere...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

[sub-wlsubj001] Applying mask to the predicted map of the left hemisphere...

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 3s
Subject processed: sub-wlsubj001
Map: eccentricity | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for lh hemisphere
--------------------------------------------------------------------------------
Processing right hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 1 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf
[sub-wlsubj001] Fast mode enabled.
[sub-wlsubj001] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj001] Converting surfaces...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.pial.gii as a surface
[sub-wlsubj001] Generating midthickness surface...
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.graymid.gii
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.graymid as a surface
[sub-wlsubj001] Computing curvature...
total integrated curvature = -3.967*4pi (-49.856) --> 5 handles
ICI = 149.7, FI = 1361.8, variation=22336.733
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.graymid.K...done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.graymid.H...done.
[sub-wlsubj001] Mid-thickness surface has been generated
[sub-wlsubj001] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj001] Running freesurfer-resample-prep...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.midthickness.surf.gii.temp33153.white.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.midthickness.surf.gii.temp33153.pial.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.sphere.reg.surf.gii as a surface
[sub-wlsubj001] Converting curvature data...
[sub-wlsubj001] Resampling native data to fsaverage space...
[sub-wlsubj001] Data resampling complete
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 19s
Subject processed: sub-wlsubj001
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_33301_a6080ceb_38857
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_RH_model.pt
Running inference for model 1...
Inference completed in 0.28 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.50 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 48s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_33301_a6080ceb_38857
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the right hemisphere...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

[sub-wlsubj001] Applying mask to the predicted map of the right hemisphere...

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 4s
Subject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_33484_76f178e4_96041
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.29 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_RH_model.pt
Running inference for model 1...
Inference completed in 0.28 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.47 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 45s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_33484_76f178e4_96041
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the right hemisphere...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

[sub-wlsubj001] Applying mask to the predicted map of the right hemisphere...

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 3s
Subject processed: sub-wlsubj001
Map: eccentricity | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for rh hemisphere
--------------------------------------------------------------------------------
Execution completed!

!ls $PATH_FREESURFER_DIR/sub-wlsubj001/deepRetinotopy

sub-wlsubj001.ROI.lh.native.label.gii
sub-wlsubj001.ROI.rh.native.label.gii
sub-wlsubj001.fs_predicted_eccentricity_lh_curvatureFeat_model.func.gii
sub-wlsubj001.fs_predicted_eccentricity_rh_curvatureFeat_model.func.gii
sub-wlsubj001.fs_predicted_polarAngle_lh_curvatureFeat_model.func.gii
sub-wlsubj001.fs_predicted_polarAngle_rh_curvatureFeat_model.func.gii
sub-wlsubj001.predicted_eccentricity_model.lh.native.func.gii
sub-wlsubj001.predicted_eccentricity_model.rh.native.func.gii
sub-wlsubj001.predicted_polarAngle_model.lh.native.func.gii
sub-wlsubj001.predicted_polarAngle_model.rh.native.func.gii

## Process single subject with an explicit output directory
! mkdir -p ../../../output && \
deepRetinotopy -s $PATH_FREESURFER_DIR -t $PATH_HCP_TEMPLATE_SURFACE -d $DATASET_NAME -m $MAPS -i sub-wlsubj001 -o ../../../output

Processing single subject: sub-wlsubj001
Log files location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Output log: deepRetinotopy_20260120_111000_output.log
Error log: deepRetinotopy_20260120_111000_error.log
--------------------------------------------------------------------------------
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------------------------------------------------
Log files: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/deepRetinotopy_20260120_111000_output.log and deepRetinotopy_20260120_111000_error.log
--------------------------------------------------------------------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-fsaverage template surfaces: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/templates
Dataset name: nyu
Maps: polarAngle eccentricity
Processing mode: Single subject (sub-wlsubj001)
Fast midthickness generation: yes
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Execution mode: Complete pipeline (Steps 1, 2, and 3)
--------------------------------------------------------------------------------
Processing left hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Processing subject: sub-wlsubj001
=== Processing Step 1 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using custom output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001
[sub-wlsubj001] Fast mode enabled.
[sub-wlsubj001] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj001] Converting surfaces...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.pial.gii as a surface
[sub-wlsubj001] Generating midthickness surface...
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.graymid.gii
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.graymid as a surface
[sub-wlsubj001] Computing curvature...
total integrated curvature = -2.905*4pi (-36.505) --> 4 handles
ICI = 155.2, FI = 1392.0, variation=22879.765
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.graymid.K...done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.graymid.H...done.
[sub-wlsubj001] Mid-thickness surface has been generated
[sub-wlsubj001] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj001] Running freesurfer-resample-prep...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.midthickness.surf.gii.temp33784.white.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.midthickness.surf.gii.temp33784.pial.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.sphere.reg.surf.gii as a surface
[sub-wlsubj001] Converting curvature data...
[sub-wlsubj001] Resampling native data to fsaverage space...
[sub-wlsubj001] Data resampling complete
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 21s
Subject processed: sub-wlsubj001
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
Output directory set to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/processed_33932_654be88b_32217
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
Created output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.29 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_LH_model.pt
Running inference for model 1...
Inference completed in 0.28 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Created output directory
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.36 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 39s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/processed_33932_654be88b_32217
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using custom output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the left hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the left hemisphere...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

[sub-wlsubj001] Transforming polar angle map of the left hemisphere...
[sub-wlsubj001] Applying mask to the predicted map of the left hemisphere...

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 4s
Subject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: lh
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
Output directory set to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/processed_34149_e86c3d60_80829
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
Created output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.29 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_LH_model.pt
Running inference for model 1...
Inference completed in 0.28 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.34 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 37s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: lh | Dataset: nyu
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/processed_34149_e86c3d60_80829
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using custom output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the left hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the left hemisphere...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

[sub-wlsubj001] Applying mask to the predicted map of the left hemisphere...

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 4s
Subject processed: sub-wlsubj001
Map: eccentricity | Model: model | Hemisphere: lh
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
eccentricity resampling completed for lh hemisphere
--------------------------------------------------------------------------------
Processing right hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Processing subject: sub-wlsubj001
=== Processing Step 1 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using custom output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001
[sub-wlsubj001] Fast mode enabled.
[sub-wlsubj001] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj001] Converting surfaces...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.pial.gii as a surface
[sub-wlsubj001] Generating midthickness surface...
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.graymid.gii
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.graymid as a surface
[sub-wlsubj001] Computing curvature...
total integrated curvature = -3.967*4pi (-49.856) --> 5 handles
ICI = 149.7, FI = 1361.8, variation=22336.733
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.graymid.K...done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.graymid.H...done.
[sub-wlsubj001] Mid-thickness surface has been generated
[sub-wlsubj001] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj001] Running freesurfer-resample-prep...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.midthickness.surf.gii.temp34386.white.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.midthickness.surf.gii.temp34386.pial.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.sphere.reg.surf.gii as a surface
[sub-wlsubj001] Converting curvature data...
[sub-wlsubj001] Resampling native data to fsaverage space...
[sub-wlsubj001] Data resampling complete
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 18s
Subject processed: sub-wlsubj001
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
Output directory set to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/processed_34534_299ceefb_46356
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
Created output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_RH_model.pt
Running inference for model 1...
Inference completed in 0.28 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.34 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 37s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: rh | Dataset: nyu
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/processed_34534_299ceefb_46356
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using custom output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the right hemisphere...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

[sub-wlsubj001] Applying mask to the predicted map of the right hemisphere...

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 4s
Subject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: rh
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
Output directory set to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/processed_34721_5dd3832e_93594
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
Created output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.29 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_RH_model.pt
Running inference for model 1...
Inference completed in 0.28 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.34 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 38s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: rh | Dataset: nyu
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/processed_34721_5dd3832e_93594
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using custom output directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the right hemisphere...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

[sub-wlsubj001] Applying mask to the predicted map of the right hemisphere...

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 4s
Subject processed: sub-wlsubj001
Map: eccentricity | Model: model | Hemisphere: rh
Output location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output
===============================================
eccentricity resampling completed for rh hemisphere
--------------------------------------------------------------------------------
Execution completed!
All output files have been saved to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/output

!ls ../../../output/sub-wlsubj001/

deepRetinotopy	surf

Running deepRetinotopy for multiple subjects

If no subject is specified, all subjects within the FreeSurfer directory will be processed. However, for optimal speed, parallelising the processing for multiple subjects across multiple cores is preferred.

## Determine how many cores you have available
os.environ['NUMBER_OF_CORES'] = str(os.cpu_count() - 1)

%%bash

SUBJECT_LIST=(sub-wlsubj001 sub-wlsubj004 sub-wlsubj006 sub-wlsubj007)

process_subject() {
    local subject=$1
    echo "Processing subject: $subject"
    deepRetinotopy -s $PATH_FREESURFER_DIR -t $PATH_HCP_TEMPLATE_SURFACE -d $DATASET_NAME -m $MAPS -i "$subject"
}

export -f process_subject

printf "%s\n" "${SUBJECT_LIST[@]}" | xargs -P "$NUMBER_OF_CORES" -I {} bash -c 'process_subject "{}"'

Processing subject: sub-wlsubj001
Processing subject: sub-wlsubj004
Processing subject: sub-wlsubj006
Processing subject: sub-wlsubj007
Processing single subject: sub-wlsubj004
Processing single subject: sub-wlsubj001
Processing single subject: sub-wlsubj006
Processing single subject: sub-wlsubj007
Log files location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs
Output log: deepRetinotopy_20260120_111359_output.log
Error log: deepRetinotopy_20260120_111359_error.log
--------------------------------------------------------------------------------
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------------------------------------------------
Log files: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260120_111359_output.log and deepRetinotopy_20260120_111359_error.log
--------------------------------------------------------------------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-fsaverage template surfaces: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/templates
Dataset name: nyu
Maps: polarAngle eccentricity
Processing mode: Single subject (sub-wlsubj001)
Fast midthickness generation: yes
Output mode: In-place (within FreeSurfer directory structure)
Execution mode: Complete pipeline (Steps 1, 2, and 3)
--------------------------------------------------------------------------------
Processing left hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Log files location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs
Output log: deepRetinotopy_20260120_111359_output.log
Error log: deepRetinotopy_20260120_111359_error.log
--------------------------------------------------------------------------------
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------------------------------------------------
Log files: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260120_111359_output.log and deepRetinotopy_20260120_111359_error.log
--------------------------------------------------------------------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-fsaverage template surfaces: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/templates
Dataset name: nyu
Maps: polarAngle eccentricity
Processing mode: Single subject (sub-wlsubj006)
Fast midthickness generation: yes
Output mode: In-place (within FreeSurfer directory structure)
Execution mode: Complete pipeline (Steps 1, 2, and 3)
--------------------------------------------------------------------------------
Processing left hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Log files location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs
Output log: deepRetinotopy_20260120_111359_output.log
Error log: deepRetinotopy_20260120_111359_error.log
--------------------------------------------------------------------------------
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------------------------------------------------
Log files: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260120_111359_output.log and deepRetinotopy_20260120_111359_error.log
--------------------------------------------------------------------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-fsaverage template surfaces: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/templates
Dataset name: nyu
Maps: polarAngle eccentricity
Processing mode: Single subject (sub-wlsubj004)
Fast midthickness generation: yes
Output mode: In-place (within FreeSurfer directory structure)
Execution mode: Complete pipeline (Steps 1, 2, and 3)
--------------------------------------------------------------------------------
Processing left hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Log files location: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs
Output log: deepRetinotopy_20260120_111359_output.log
Error log: deepRetinotopy_20260120_111359_error.log
--------------------------------------------------------------------------------
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------------------------------------------------
Log files: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260120_111359_output.log and deepRetinotopy_20260120_111359_error.log
--------------------------------------------------------------------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-fsaverage template surfaces: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/templates
Dataset name: nyu
Maps: polarAngle eccentricity
Processing mode: Single subject (sub-wlsubj007)
Fast midthickness generation: yes
Output mode: In-place (within FreeSurfer directory structure)
Execution mode: Complete pipeline (Steps 1, 2, and 3)
--------------------------------------------------------------------------------
Processing left hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Hemisphere: lh
Processing single subject: sub-wlsubj007
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
Hemisphere: lh
Processing single subject: sub-wlsubj006
=== Processing Step 1 for subject: sub-wlsubj001 ===
Output mode: In-place (within FreeSurfer directory structure)
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf
Hemisphere: lh
Processing single subject: sub-wlsubj004
Output mode: In-place (within FreeSurfer directory structure)
[sub-wlsubj001] Fast mode enabled.
[sub-wlsubj001] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj001] Mid-thickness surface and curvature data already available
[sub-wlsubj001] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj001] Resampled curvature data already available
Processing subject: sub-wlsubj006
=== Processing Step 1 for subject: sub-wlsubj006 ===
[sub-wlsubj006] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf
Processing subject: sub-wlsubj007
=== Processing Step 1 for subject: sub-wlsubj007 ===
[sub-wlsubj007] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf
Processing subject: sub-wlsubj004
=== Processing Step 1 for subject: sub-wlsubj004 ===
[sub-wlsubj004] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf
=== Subject sub-wlsubj001 completed in 0 minutes ===
[sub-wlsubj006] Fast mode enabled.
[sub-wlsubj006] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj006] Converting surfaces...
[sub-wlsubj007] Fast mode enabled.
[sub-wlsubj007] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj007] Converting surfaces...
[sub-wlsubj004] Fast mode enabled.
[sub-wlsubj004] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj004] Converting surfaces...

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 0s
Subject processed: sub-wlsubj001
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/lh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/lh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/lh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/lh.pial.gii as a surface
[sub-wlsubj006] Generating midthickness surface...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/lh.pial.gii as a surface
[sub-wlsubj007] Generating midthickness surface...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/lh.pial.gii as a surface
[sub-wlsubj004] Generating midthickness surface...
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/lh.graymid.gii
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/lh.graymid.gii
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/lh.graymid.gii
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/lh.graymid as a surface
[sub-wlsubj006] Computing curvature...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/lh.graymid as a surface
[sub-wlsubj007] Computing curvature...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/lh.graymid as a surface
[sub-wlsubj004] Computing curvature...
[sub-wlsubj006] Mid-thickness surface has been generated
[sub-wlsubj006] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj006] Running freesurfer-resample-prep...
[sub-wlsubj007] Mid-thickness surface has been generated
[sub-wlsubj007] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj007] Running freesurfer-resample-prep...
[sub-wlsubj004] Mid-thickness surface has been generated
[sub-wlsubj004] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj004] Running freesurfer-resample-prep...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/lh.midthickness.surf.gii.temp35352.white.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/lh.midthickness.surf.gii.temp35357.white.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/lh.midthickness.surf.gii.temp35474.white.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/lh.midthickness.surf.gii.temp35352.pial.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/lh.midthickness.surf.gii.temp35357.pial.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/lh.midthickness.surf.gii.temp35474.pial.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/lh.sphere.reg.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/lh.sphere.reg.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/lh.sphere.reg.surf.gii as a surface
[sub-wlsubj006] Converting curvature data...
[sub-wlsubj007] Converting curvature data...
[sub-wlsubj006] Resampling native data to fsaverage space...
[sub-wlsubj007] Resampling native data to fsaverage space...
[sub-wlsubj004] Converting curvature data...
[sub-wlsubj004] Resampling native data to fsaverage space...
[sub-wlsubj006] Data resampling complete
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 24s
Subject processed: sub-wlsubj006
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
[sub-wlsubj007] Data resampling complete
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 24s
Subject processed: sub-wlsubj007
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
[sub-wlsubj004] Data resampling complete
=== Subject sub-wlsubj004 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 26s
Subject processed: sub-wlsubj004
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_35174_a7574882_53333
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_LH_model.pt
Running inference for model 1...
Inference completed in 0.29 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.38 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 40s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_35174_a7574882_53333
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the left hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the left hemisphere...
[sub-wlsubj001] Transforming polar angle map of the left hemisphere...
[sub-wlsubj001] Applying mask to the predicted map of the left hemisphere...
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 6s
Subject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_35761_54b73087_73146
Processing single subject: sub-wlsubj006
Found 1 subjects to process: ['sub-wlsubj006']
Final subject list after validation: 1 subjects: ['sub-wlsubj006']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_LH_model.pt
Running inference for model 1...
Inference completed in 0.30 minutes
Saving predictions for 1 subjects...
[sub-wlsubj006] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Created output directory
[sub-wlsubj006] Completed in 0.0s
Model 1 processing completed in 0.37 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 40s
Subject processed: sub-wlsubj006
Prediction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_35761_54b73087_73146
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_35764_cd240f4b_73145
Processing single subject: sub-wlsubj007
Found 1 subjects to process: ['sub-wlsubj007']
Final subject list after validation: 1 subjects: ['sub-wlsubj007']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_LH_model.pt
Running inference for model 1...
Inference completed in 0.31 minutes
Saving predictions for 1 subjects...
[sub-wlsubj007] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Created output directory
[sub-wlsubj007] Completed in 0.0s
Model 1 processing completed in 0.37 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 40s
Subject processed: sub-wlsubj007
Prediction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_35764_cd240f4b_73145
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: lh
Processing single subject: sub-wlsubj006
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj006
=== Processing Step 3 for subject: sub-wlsubj006 ===
[sub-wlsubj006] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Resampling ROI from fsaverage to native space for the left hemisphere...
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: lh
Processing single subject: sub-wlsubj007
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj007
=== Processing Step 3 for subject: sub-wlsubj007 ===
[sub-wlsubj007] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Resampling ROI from fsaverage to native space for the left hemisphere...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_35860_c726c8da_76588
Processing single subject: sub-wlsubj004
Found 1 subjects to process: ['sub-wlsubj004']
Final subject list after validation: 1 subjects: ['sub-wlsubj004']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_LH_model.pt
Running inference for model 1...
Inference completed in 0.30 minutes
Saving predictions for 1 subjects...
[sub-wlsubj004] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Created output directory
[sub-wlsubj004] Completed in 0.0s
Model 1 processing completed in 0.35 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 39s
Subject processed: sub-wlsubj004
Prediction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_35860_c726c8da_76588
[sub-wlsubj006] Resampling predicted map from fsaverage to native space for the left hemisphere...
[sub-wlsubj007] Resampling predicted map from fsaverage to native space for the left hemisphere...
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: lh
Processing single subject: sub-wlsubj004
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj004
=== Processing Step 3 for subject: sub-wlsubj004 ===
[sub-wlsubj004] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Resampling ROI from fsaverage to native space for the left hemisphere...
[sub-wlsubj006] Transforming polar angle map of the left hemisphere...
[sub-wlsubj007] Transforming polar angle map of the left hemisphere...
[sub-wlsubj006] Applying mask to the predicted map of the left hemisphere...
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 4s
Subject processed: sub-wlsubj006
Map: polarAngle | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
[sub-wlsubj007] Applying mask to the predicted map of the left hemisphere...
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 5s
Subject processed: sub-wlsubj007
Map: polarAngle | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
[sub-wlsubj004] Resampling predicted map from fsaverage to native space for the left hemisphere...
[sub-wlsubj004] Transforming polar angle map of the left hemisphere...
[sub-wlsubj004] Applying mask to the predicted map of the left hemisphere...
=== Subject sub-wlsubj004 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 4s
Subject processed: sub-wlsubj004
Map: polarAngle | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_36230_c4acce7c_5629
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_LH_model.pt
Running inference for model 1...
Inference completed in 0.29 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.34 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 38s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_36230_c4acce7c_5629
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the left hemisphere...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the left hemisphere...
[sub-wlsubj001] Applying mask to the predicted map of the left hemisphere...
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 5s
Subject processed: sub-wlsubj001
Map: eccentricity | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for lh hemisphere
--------------------------------------------------------------------------------
Processing right hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 1 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf
[sub-wlsubj001] Fast mode enabled.
[sub-wlsubj001] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj001] Mid-thickness surface and curvature data already available
[sub-wlsubj001] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj001] Resampled curvature data already available
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 0s
Subject processed: sub-wlsubj001
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_36571_e73ea1c4_24011
Processing single subject: sub-wlsubj006
Found 1 subjects to process: ['sub-wlsubj006']
Final subject list after validation: 1 subjects: ['sub-wlsubj006']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_LH_model.pt
Running inference for model 1...
Inference completed in 0.31 minutes
Saving predictions for 1 subjects...
[sub-wlsubj006] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Completed in 0.0s
Model 1 processing completed in 0.38 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 40s
Subject processed: sub-wlsubj006
Prediction type: eccentricity | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_36571_e73ea1c4_24011
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_36580_9ff1faf2_24006
Processing single subject: sub-wlsubj007
Found 1 subjects to process: ['sub-wlsubj007']
Final subject list after validation: 1 subjects: ['sub-wlsubj007']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_LH_model.pt
Running inference for model 1...
Inference completed in 0.31 minutes
Saving predictions for 1 subjects...
[sub-wlsubj007] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Completed in 0.0s
Model 1 processing completed in 0.38 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 40s
Subject processed: sub-wlsubj007
Prediction type: eccentricity | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_36580_9ff1faf2_24006
[Step 3] Resampling predictions to native space...
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: lh
Processing single subject: sub-wlsubj006
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj006
=== Processing Step 3 for subject: sub-wlsubj006 ===
[sub-wlsubj006] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Resampling ROI from fsaverage to native space for the left hemisphere...
Model: model
Map: eccentricity
Hemisphere: lh
Processing single subject: sub-wlsubj007
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj007
=== Processing Step 3 for subject: sub-wlsubj007 ===
[sub-wlsubj007] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Resampling ROI from fsaverage to native space for the left hemisphere...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_36782_bde0ef5c_26790
Processing single subject: sub-wlsubj004
Found 1 subjects to process: ['sub-wlsubj004']
Final subject list after validation: 1 subjects: ['sub-wlsubj004']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_LH_model.pt
Running inference for model 1...
Inference completed in 0.30 minutes
Saving predictions for 1 subjects...
[sub-wlsubj004] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Completed in 0.0s
Model 1 processing completed in 0.36 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 39s
Subject processed: sub-wlsubj004
Prediction type: eccentricity | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_36782_bde0ef5c_26790
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: lh
Processing single subject: sub-wlsubj004
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj004
=== Processing Step 3 for subject: sub-wlsubj004 ===
[sub-wlsubj004] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Resampling ROI from fsaverage to native space for the left hemisphere...
[sub-wlsubj006] Resampling predicted map from fsaverage to native space for the left hemisphere...
[sub-wlsubj007] Resampling predicted map from fsaverage to native space for the left hemisphere...
[sub-wlsubj004] Resampling predicted map from fsaverage to native space for the left hemisphere...
[sub-wlsubj006] Applying mask to the predicted map of the left hemisphere...
[sub-wlsubj007] Applying mask to the predicted map of the left hemisphere...
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 6s
Subject processed: sub-wlsubj006
Map: eccentricity | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for lh hemisphere
--------------------------------------------------------------------------------
Processing right hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Hemisphere: rh
Processing single subject: sub-wlsubj006
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj006
=== Processing Step 1 for subject: sub-wlsubj006 ===
[sub-wlsubj006] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf
[sub-wlsubj006] Fast mode enabled.
[sub-wlsubj006] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj006] Converting surfaces...
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 6s
Subject processed: sub-wlsubj007
Map: eccentricity | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for lh hemisphere
--------------------------------------------------------------------------------
Processing right hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Hemisphere: rh
Processing single subject: sub-wlsubj007
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj007
=== Processing Step 1 for subject: sub-wlsubj007 ===
[sub-wlsubj007] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf
[sub-wlsubj007] Fast mode enabled.
[sub-wlsubj007] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj007] Converting surfaces...
[sub-wlsubj004] Applying mask to the predicted map of the left hemisphere...
=== Subject sub-wlsubj004 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 6s
Subject processed: sub-wlsubj004
Map: eccentricity | Model: model | Hemisphere: lh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for lh hemisphere
--------------------------------------------------------------------------------
Processing right hemisphere
--------------------------------------------------------------------------------
[Step 1] Generating mid-thickness surface and curvature data...
Hemisphere: rh
Processing single subject: sub-wlsubj004
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj004
=== Processing Step 1 for subject: sub-wlsubj004 ===
[sub-wlsubj004] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf
[sub-wlsubj004] Fast mode enabled.
[sub-wlsubj004] [Step 1.1] Generating mid-thickness surface and curvature data if not available...
[sub-wlsubj004] Converting surfaces...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/rh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/rh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/rh.white.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/rh.pial.gii as a surface
[sub-wlsubj006] Generating midthickness surface...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/rh.pial.gii as a surface
[sub-wlsubj007] Generating midthickness surface...
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/rh.graymid.gii
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/rh.graymid.gii
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/rh.pial.gii as a surface
[sub-wlsubj004] Generating midthickness surface...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/rh.graymid as a surface
[sub-wlsubj007] Computing curvature...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/rh.graymid as a surface
[sub-wlsubj006] Computing curvature...
Midthickness surface saved at /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/rh.graymid.gii
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/rh.graymid as a surface
[sub-wlsubj004] Computing curvature...
[sub-wlsubj007] Mid-thickness surface has been generated
[sub-wlsubj007] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj007] Running freesurfer-resample-prep...
[sub-wlsubj006] Mid-thickness surface has been generated
[sub-wlsubj006] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj006] Running freesurfer-resample-prep...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/rh.midthickness.surf.gii.temp37590.white.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/rh.midthickness.surf.gii.temp37560.white.surf.gii as a surface
[sub-wlsubj004] Mid-thickness surface has been generated
[sub-wlsubj004] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj004] Running freesurfer-resample-prep...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/rh.midthickness.surf.gii.temp37590.pial.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/rh.midthickness.surf.gii.temp37560.pial.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/rh.midthickness.surf.gii.temp37684.white.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/rh.sphere.reg.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/rh.sphere.reg.surf.gii as a surface
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/rh.midthickness.surf.gii.temp37684.pial.surf.gii as a surface
[sub-wlsubj007] Converting curvature data...
[sub-wlsubj006] Converting curvature data...
Saving /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/rh.sphere.reg.surf.gii as a surface
[sub-wlsubj006] Resampling native data to fsaverage space...
[sub-wlsubj007] Resampling native data to fsaverage space...
[sub-wlsubj006] Data resampling complete
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 22s
Subject processed: sub-wlsubj006
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
[sub-wlsubj007] Data resampling complete
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 22s
Subject processed: sub-wlsubj007
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
[sub-wlsubj004] Converting curvature data...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_37065_0d06a690_56064
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.31 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_RH_model.pt
Running inference for model 1...
Inference completed in 0.28 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.35 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 39s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_37065_0d06a690_56064
[sub-wlsubj004] Resampling native data to fsaverage space...
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj004] Data resampling complete
=== Subject sub-wlsubj004 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 25s
Subject processed: sub-wlsubj004
Output location: In-place within FreeSurfer directory
===============================================
--------------------------------------------------------------------------------
Map: polarAngle
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the right hemisphere...
[sub-wlsubj001] Applying mask to the predicted map of the right hemisphere...
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 4s
Subject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_37965_8f14f7e1_2285
Processing single subject: sub-wlsubj007
Found 1 subjects to process: ['sub-wlsubj007']
Final subject list after validation: 1 subjects: ['sub-wlsubj007']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_RH_model.pt
Running inference for model 1...
Inference completed in 0.30 minutes
Saving predictions for 1 subjects...
[sub-wlsubj007] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Completed in 0.0s
Model 1 processing completed in 0.37 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 40s
Subject processed: sub-wlsubj007
Prediction type: polarAngle | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_37965_8f14f7e1_2285
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_37962_c0fc9759_2285
Processing single subject: sub-wlsubj006
Found 1 subjects to process: ['sub-wlsubj006']
Final subject list after validation: 1 subjects: ['sub-wlsubj006']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_RH_model.pt
Running inference for model 1...
Inference completed in 0.30 minutes
Saving predictions for 1 subjects...
[sub-wlsubj006] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Completed in 0.0s
Model 1 processing completed in 0.37 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 40s
Subject processed: sub-wlsubj006
Prediction type: polarAngle | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_37962_c0fc9759_2285
[Step 3] Resampling predictions to native space...
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: rh
Processing single subject: sub-wlsubj007
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj007
=== Processing Step 3 for subject: sub-wlsubj007 ===
[sub-wlsubj007] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Resampling ROI from fsaverage to native space for the right hemisphere...
Model: model
Map: polarAngle
Hemisphere: rh
Processing single subject: sub-wlsubj006
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj006
=== Processing Step 3 for subject: sub-wlsubj006 ===
[sub-wlsubj006] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Resampling ROI from fsaverage to native space for the right hemisphere...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAngle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38175_1b3211be_4816
Processing single subject: sub-wlsubj004
Found 1 subjects to process: ['sub-wlsubj004']
Final subject list after validation: 1 subjects: ['sub-wlsubj004']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_polarAngle_RH_model.pt
Running inference for model 1...
Inference completed in 0.29 minutes
Saving predictions for 1 subjects...
[sub-wlsubj004] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Completed in 0.0s
Model 1 processing completed in 0.36 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 39s
Subject processed: sub-wlsubj004
Prediction type: polarAngle | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38175_1b3211be_4816
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: rh
Processing single subject: sub-wlsubj004
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj004
=== Processing Step 3 for subject: sub-wlsubj004 ===
[sub-wlsubj004] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj007] Resampling predicted map from fsaverage to native space for the right hemisphere...
[sub-wlsubj006] Resampling predicted map from fsaverage to native space for the right hemisphere...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38253_8fbad016_6291
Processing single subject: sub-wlsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subjects: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_RH_model.pt
Running inference for model 1...
Inference completed in 0.30 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.37 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 40s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38253_8fbad016_6291
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj001
=== Processing Step 3 for subject: sub-wlsubj001 ===
[sub-wlsubj001] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj007] Applying mask to the predicted map of the right hemisphere...
[sub-wlsubj006] Applying mask to the predicted map of the right hemisphere...
[sub-wlsubj004] Resampling predicted map from fsaverage to native space for the right hemisphere...
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 5s
Subject processed: sub-wlsubj007
Map: polarAngle | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 5s
Subject processed: sub-wlsubj006
Map: polarAngle | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
[sub-wlsubj001] Resampling predicted map from fsaverage to native space for the right hemisphere...
[sub-wlsubj004] Applying mask to the predicted map of the right hemisphere...
=== Subject sub-wlsubj004 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 5s
Subject processed: sub-wlsubj004
Map: polarAngle | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
--------------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
[sub-wlsubj001] Applying mask to the predicted map of the right hemisphere...
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 5s
Subject processed: sub-wlsubj001
Map: eccentricity | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for rh hemisphere
--------------------------------------------------------------------------------
Execution completed!
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38737_9e672a03_54008
Processing single subject: sub-wlsubj006
Found 1 subjects to process: ['sub-wlsubj006']
Final subject list after validation: 1 subjects: ['sub-wlsubj006']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.30 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_RH_model.pt
Running inference for model 1...
Inference completed in 0.29 minutes
Saving predictions for 1 subjects...
[sub-wlsubj006] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Completed in 0.0s
Model 1 processing completed in 0.34 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 38s
Subject processed: sub-wlsubj006
Prediction type: eccentricity | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38737_9e672a03_54008
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38735_c0d8c9a2_53975
Processing single subject: sub-wlsubj007
Found 1 subjects to process: ['sub-wlsubj007']
Final subject list after validation: 1 subjects: ['sub-wlsubj007']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.29 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_RH_model.pt
Running inference for model 1...
Inference completed in 0.30 minutes
Saving predictions for 1 subjects...
[sub-wlsubj007] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Completed in 0.0s
Model 1 processing completed in 0.34 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 38s
Subject processed: sub-wlsubj007
Prediction type: eccentricity | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38735_c0d8c9a2_53975
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentricity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer directory structure)
===============================================
Output directory not specified, using input path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38907_5c93a608_55635
Processing single subject: sub-wlsubj004
Found 1 subjects to process: ['sub-wlsubj004']
Final subject list after validation: 1 subjects: ['sub-wlsubj004']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.29 minutes
[Step 2.2] Generating predictions with pre-trained models...
Loading model 1/1...
Using device: cpu
Loading model from: deepRetinotopy_eccentricity_RH_model.pt
Running inference for model 1...
Inference completed in 0.29 minutes
Saving predictions for 1 subjects...
[sub-wlsubj004] Saving predictions to: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Completed in 0.0s
Model 1 processing completed in 0.32 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 37s
Subject processed: sub-wlsubj004
Prediction type: eccentricity | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38907_5c93a608_55635
[Step 3] Resampling predictions to native space...
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: rh
Processing single subject: sub-wlsubj007
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj007
=== Processing Step 3 for subject: sub-wlsubj007 ===
[sub-wlsubj007] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Resampling ROI from fsaverage to native space for the right hemisphere...
Model: model
Map: eccentricity
Hemisphere: rh
Processing single subject: sub-wlsubj006
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj006
=== Processing Step 3 for subject: sub-wlsubj006 ===
[sub-wlsubj006] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Resampling ROI from fsaverage to native space for the right hemisphere...
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: rh
Processing single subject: sub-wlsubj004
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj004
=== Processing Step 3 for subject: sub-wlsubj004 ===
[sub-wlsubj004] Using FreeSurfer directory: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj006] Resampling predicted map from fsaverage to native space for the right hemisphere...
[sub-wlsubj007] Resampling predicted map from fsaverage to native space for the right hemisphere...
[sub-wlsubj004] Resampling predicted map from fsaverage to native space for the right hemisphere...
[sub-wlsubj007] Applying mask to the predicted map of the right hemisphere...
[sub-wlsubj006] Applying mask to the predicted map of the right hemisphere...
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 5s
Subject processed: sub-wlsubj007
Map: eccentricity | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for rh hemisphere
--------------------------------------------------------------------------------
Execution completed!
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 5s
Subject processed: sub-wlsubj006
Map: eccentricity | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for rh hemisphere
--------------------------------------------------------------------------------
Execution completed!
[sub-wlsubj004] Applying mask to the predicted map of the right hemisphere...
=== Subject sub-wlsubj004 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 6s
Subject processed: sub-wlsubj004
Map: eccentricity | Model: model | Hemisphere: rh
Output location: In-place within FreeSurfer directory
===============================================
eccentricity resampling completed for rh hemisphere
--------------------------------------------------------------------------------
Execution completed!

** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
total integrated curvature = -11.237*4pi (-141.203) --> 12 handles
ICI = 147.3, FI = 1471.0, variation=23704.286
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/lh.graymid.K...total integrated curvature = -0.559*4pi (-7.022) --> 2 handles
done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/lh.graymid.H...ICI = 144.8, FI = 1382.4, variation=22337.118
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/lh.graymid.K...done.
done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/lh.graymid.H...done.
total integrated curvature = -7.220*4pi (-90.731) --> 8 handles
ICI = 151.6, FI = 1563.0, variation=24939.408
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/lh.graymid.K...done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/lh.graymid.H...done.
Processing...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Done!
Processing...
Processing...
Processing...
Done!
Done!
Done!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy/sub-wlsubj006.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy/sub-wlsubj007.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy/sub-wlsubj004.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Done!
Processing...
Processing...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
Done!
Done!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!


WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy/sub-wlsubj006.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy/sub-wlsubj007.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy/sub-wlsubj004.ROI.lh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!
Done!
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
total integrated curvature = -0.184*4pi (-2.317) --> 1 handles
ICI = 151.2, FI = 1466.0, variation=23585.355
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/rh.graymid.K...done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/surf/rh.graymid.H...done.
total integrated curvature = -10.888*4pi (-136.823) --> 12 handles
ICI = 152.0, FI = 1487.7, variation=24085.999
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/rh.graymid.K...done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/surf/rh.graymid.H...done.
total integrated curvature = -8.002*4pi (-100.554) --> 9 handles
ICI = 152.9, FI = 1618.7, variation=25701.339
writing Gaussian curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/rh.graymid.K...done.
writing mean curvature to /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/surf/rh.graymid.H...done.
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!
Processing...
Processing...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Processing...
Done!
Done!
Done!
Done!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!


WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy/sub-wlsubj007.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!


WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy/sub-wlsubj006.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy/sub-wlsubj004.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An issue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An issue occurred while importing 'torch-sparse'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: version `GLIBC_2.29' not found (required by /opt/miniconda-latest/lib/python3.12/site-packages/libpyg.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Processing...
Processing...
Done!
Done!
Done!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!


WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy/sub-wlsubj007.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy/sub-wlsubj006.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/Git_repositories/neurodeskedu/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy/sub-wlsubj004.ROI.rh.native.label.gii contains data array with NIFTI_INTENT_LABEL !!!

!ls ./sub-wlsubj004/deepRetinotopy

sub-wlsubj004.ROI.lh.native.label.gii
sub-wlsubj004.ROI.rh.native.label.gii
sub-wlsubj004.fs_predicted_eccentricity_lh_curvatureFeat_model.func.gii
sub-wlsubj004.fs_predicted_eccentricity_rh_curvatureFeat_model.func.gii
sub-wlsubj004.fs_predicted_polarAngle_lh_curvatureFeat_model.func.gii
sub-wlsubj004.fs_predicted_polarAngle_rh_curvatureFeat_model.func.gii
sub-wlsubj004.predicted_eccentricity_model.lh.native.func.gii
sub-wlsubj004.predicted_eccentricity_model.rh.native.func.gii
sub-wlsubj004.predicted_polarAngle_model.lh.native.func.gii
sub-wlsubj004.predicted_polarAngle_model.rh.native.func.gii

Maps visualization

Finally, we can visualize the predicted maps in the individual’s native space using nilearn.

from nilearn import plotting
from ipywidgets import Dropdown, interact
import nibabel as nib
import numpy as np
from IPython.display import display


def plot_data(subject, retinotopic_map):
    background = np.array(nib.load(f"./{subject}/surf/lh.graymid.H.gii").agg_data())[:]
    background[background < 0] = -1
    background[background > 1] = 1
    threshold = 1
    data = np.array(nib.load(f"./{subject}/deepRetinotopy/{subject}.predicted_{retinotopic_map}_model.lh.native.func.gii").agg_data())[:]
    data[data != 0] = data[data != 0] + threshold
    if retinotopic_map == 'eccentricity':
        max_value = 8
    else: 
        max_value = 360
    view = plotting.view_surf(
        surf_mesh=f"./{subject}/surf/lh.midthickness.surf.gii",
        surf_map=np.reshape(data[:], (-1)),
        cmap="gist_rainbow_r", black_bg=False, symmetric_cmap=False, bg_map = background,
        threshold=threshold, vmax=max_value + threshold, vmin = threshold)
    return view

subjects = ['sub-wlsubj001', 'sub-wlsubj004', 'sub-wlsubj006', 'sub-wlsubj007']
retinotopic_maps = ['eccentricity', 'polarAngle']

@interact(subject = subjects, retinotopic_map = retinotopic_maps)
def plot1(subject, retinotopic_map):
    view = plot_data(subject, retinotopic_map)
    display(view)

from IPython.display import Image, display, Markdown

display(Markdown("### Eccentricity Map"))
Image(filename='../../../../../../static/examples/functional_imaging/deepretinotopy/deepretinotopy_eccentricity.png')

Eccentricity Map

display(Markdown("### Polar Angle Map"))
Image(filename='../../../../../../static/examples/functional_imaging/deepretinotopy/deepretinotopy_polarAngle.png')

Polar Angle Map

Dependencies in Jupyter/Python

• Using the package watermark to document system environment and software versions used in this notebook

%load_ext watermark

%watermark
%watermark --iversions

Last updated: 2025-11-13T00:57:44.290157+00:00

Python implementation: CPython
Python version       : 3.11.6
IPython version      : 8.16.1

Compiler    : GCC 12.3.0
OS          : Linux
Release     : 5.4.0-204-generic
Machine     : x86_64
Processor   : x86_64
CPU cores   : 32
Architecture: 64bit

nilearn   : 0.11.1
ipywidgets: 8.1.2
numpy     : 2.2.4
IPython   : 8.16.1
nibabel   : 5.3.2