https://doi.org/10.5281/zenodo.18740132

DeepRetinotopy Toolbox

DeepRetinotopy Toolbox#

Author: Fernanda Ribeiro

Date: 12 Nov 2025

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:  98%|█████████████████████▌| 134k/137k [00:01<00:00, 66.4k Objects/s]

                                                                                
Resolving:   0%|                              | 0.00/22.7k [00:00<?, ? Deltas/s]

Resolving:  11%|██▎                  | 2.50k/22.7k [00:00<00:00, 24.8k Deltas/s]

Resolving:  33%|██████▉              | 7.49k/22.7k [00:00<00:00, 39.2k Deltas/s]

Resolving:  55%|███████████▌         | 12.5k/22.7k [00:00<00:00, 43.4k Deltas/s]

Resolving:  76%|███████████████▉     | 17.2k/22.7k [00:00<00:00, 44.4k Deltas/s]

Resolving:  96%|████████████████████▏| 21.8k/22.7k [00:00<00:00, 44.4k 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
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get(ok): derivatives/freesurfer/sub-wlsubj067/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj067/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj122/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj109/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-wlsubj105/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj105/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj105/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj105/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj105/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj105/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj105/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj105/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj105/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj105/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj087/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj126/surf/rh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/surf/lh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/surf/lh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/surf/lh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/surf/lh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/surf/lh.thickness (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/surf/rh.pial (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/surf/rh.white (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/surf/rh.sphere (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/surf/rh.sphere.reg (file) [from s3-PUBLIC...]
get(ok): derivatives/freesurfer/sub-wlsubj118/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 -nc 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 -nc 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

--2026-04-09 06:22:55--  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)...
4.237.22.38
Connecting to github.com (github.com)|4.237.22.38|: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]
--2026-04-09 06:22:56--  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)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|: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 0.008s  

2026-04-09 06:22:56 (87.4 MB/s) - ‘fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii’ saved [720487/720487]

--2026-04-09 06:22:56--  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)... 4.237.22.38
Connecting to github.com (github.com)|4.237.22.38|: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]
--2026-04-09 06:22:56--  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)... 185.199.110.133, 185.199.108.133, 185.199.111.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|: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 0.009s  

2026-04-09 06:22:57 (79.3 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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs
Output log: deepRetinotopy_20260409_062259_output.log
Error log: deepRetinotopy_20260409_062259_error.log
--------------------------------------------------------------------------------
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------------------------------------------------
Log files: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260409_062259_output.log and deepRetinotopy_20260409_062259_error.log
--------------------------------------------------------------------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-fsaverage template surfaces: /home/jovyan/workspace/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/workspace/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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.white.gii as a surface
Saving /home/jovyan/workspace/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/workspace/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/workspace/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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.graymid.K...
done.
writing mean curvature to /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.midthickness.surf.gii.temp33293.white.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/lh.midthickness.surf.gii.temp33293.pial.surf.gii as a surface
Saving /home/jovyan/workspace/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 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 27s
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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_33478_8af55c84_37114
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: 0.38 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 0.50 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/workspace/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 0.68 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 1m 3s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_33478_8af55c84_37114
[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/workspace/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/workspace/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 10s
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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_33939_6528cd0f_19252
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: 0.37 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 0.50 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.67 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 1m 2s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_33939_6528cd0f_19252
[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/workspace/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/workspace/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 9s
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/workspace/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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.white.gii as a surface
Saving /home/jovyan/workspace/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/workspace/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/workspace/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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.graymid.K...done.
writing mean curvature to /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.midthickness.surf.gii.temp34359.white.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/surf/rh.midthickness.surf.gii.temp34359.pial.surf.gii as a surface
Saving /home/jovyan/workspace/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 23s
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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_34547_926fe592_22100
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: 0.36 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 0.50 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.69 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 1m 3s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_34547_926fe592_22100
[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/workspace/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/workspace/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 8s
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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_34903_63ad0467_676
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: 0.38 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 0.51 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.68 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 1m 3s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
===============================================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_34903_63ad0467_676
[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/workspace/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/workspace/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 10s
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/workspace/books/examples/functional_imaging/data/output
Output log: deepRetinotopy_20260409_062937_output.log
Error log: deepRetinotopy_20260409_062937_error.log
--------------------------------------------------------------------------------
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------------------------------------------------
Log files: /home/jovyan/workspace/books/examples/functional_imaging/data/output/deepRetinotopy_20260409_062937_output.log and deepRetinotopy_20260409_062937_error.log
--------------------------------------------------------------------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-fsaverage template surfaces: /home/jovyan/workspace/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/workspace/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/workspace/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/workspace/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/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.white.gii as a surface
Saving /home/jovyan/workspace/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/workspace/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/workspace/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/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.graymid.K...done.
writing mean curvature to /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.midthickness.surf.gii.temp35394.white.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/lh.midthickness.surf.gii.temp35394.pial.surf.gii as a surface
Saving /home/jovyan/workspace/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 23s
Subject processed: sub-wlsubj001
Output location: /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/output
===============================================
Output directory set to: /home/jovyan/workspace/books/examples/functional_imaging/data/output
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/output
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/data/output/processed_35573_a17dab4b_7163
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/workspace/books/examples/functional_imaging/data/output
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.37 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 0.51 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/workspace/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 0.56 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 55s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: /home/jovyan/workspace/books/examples/functional_imaging/data/output
===============================================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_imaging/data/output/processed_35573_a17dab4b_7163
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/workspace/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/workspace/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/workspace/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 11s
Subject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: lh
Output location: /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/output
===============================================
Output directory set to: /home/jovyan/workspace/books/examples/functional_imaging/data/output
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/output
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/data/output/processed_35956_d1fa535d_81597
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/workspace/books/examples/functional_imaging/data/output
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.37 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 0.53 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.59 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 57s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: lh | Dataset: nyu
Output location: /home/jovyan/workspace/books/examples/functional_imaging/data/output
===============================================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_imaging/data/output/processed_35956_d1fa535d_81597
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/workspace/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/workspace/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/workspace/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 10s
Subject processed: sub-wlsubj001
Map: eccentricity | Model: model | Hemisphere: lh
Output location: /home/jovyan/workspace/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/workspace/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/workspace/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/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.white.gii as a surface
Saving /home/jovyan/workspace/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/workspace/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/workspace/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/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.graymid.K...
done.
writing mean curvature to /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.midthickness.surf.gii.temp36368.white.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/surf/rh.midthickness.surf.gii.temp36368.pial.surf.gii as a surface
Saving /home/jovyan/workspace/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 27s
Subject processed: sub-wlsubj001
Output location: /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/output
===============================================
Output directory set to: /home/jovyan/workspace/books/examples/functional_imaging/data/output
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/output
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/data/output/processed_36555_c999e5e8_84607
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/workspace/books/examples/functional_imaging/data/output
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.38 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 0.51 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.55 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 55s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: rh | Dataset: nyu
Output location: /home/jovyan/workspace/books/examples/functional_imaging/data/output
===============================================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_imaging/data/output/processed_36555_c999e5e8_84607
[Step 3] Resampling predictions to native space...
Model: model
Map: polarAngle
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/workspace/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/workspace/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/workspace/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 11s
Subject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: rh
Output location: /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/output
===============================================
Output directory set to: /home/jovyan/workspace/books/examples/functional_imaging/data/output
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/output
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/data/output/processed_36898_9b652391_59122
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/workspace/books/examples/functional_imaging/data/output
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading time: 0.36 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 0.55 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/output/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing completed in 0.59 minutes

===============================================
[Step 2] COMPLETED!
Total execution time: 0m 57s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere: rh | Dataset: nyu
Output location: /home/jovyan/workspace/books/examples/functional_imaging/data/output
===============================================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_imaging/data/output/processed_36898_9b652391_59122
[Step 3] Resampling predictions to native space...
Model: model
Map: eccentricity
Hemisphere: rh
Processing single subject: sub-wlsubj001
Output directory: /home/jovyan/workspace/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/workspace/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/workspace/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 10s
Subject processed: sub-wlsubj001
Map: eccentricity | Model: model | Hemisphere: rh
Output location: /home/jovyan/workspace/books/examples/functional_imaging/data/output
===============================================
eccentricity resampling completed for rh hemisphere
--------------------------------------------------------------------------------
Execution completed!
All output files have been saved to: /home/jovyan/workspace/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-wlsubj006
Processing single subject: sub-wlsubj007
Processing single subject: sub-wlsubj004
Log files location: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivativ
es/freesurfer/logs
Output log: deepRetinotopy_20260409_063529_output.log
Error log: deepRetinotopy_2
0260409_063529_error.log
---------------------------------------------------------------------------
-----
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------
------------------------------------------
Log files: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260409_063529_output.log and d
eepRetinotopy_20260409_063529_error.log
------------------------------------------------------------
--------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/workspa
ce/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-
fsaverage template surfaces: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/
templates
Dataset name: nyu
Maps: polarAngle eccentricity
Processing mode: Single subject (sub-wlsub
j007)
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/workspace/books/examples/functional_imaging/data/ds003787/derivativ
es/freesurfer/logs
Output log: deepRetinotopy_20260409_063529_output.log
Error log: deepRetinotopy_2
0260409_063529_error.log
---------------------------------------------------------------------------
-----
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------
------------------------------------------
Log files: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260409_063529_output.log and d
eepRetinotopy_20260409_063529_error.log
------------------------------------------------------------
--------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/workspa
ce/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-
fsaverage template surfaces: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/
templates
Dataset name: nyu
Maps: polarAngle eccentricity
Processing mode: Single subject (sub-wlsub
j004)
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/workspace/books/examples/functional_imaging/data/ds003787/
derivatives/freesurfer/logs
Output log: deepRetinotopy_20260409_063529_output.log
Error log: deepRet
inotopy_20260409_063529_error.log
------------------------------------------------------------------
--------------
DeepRetinotopy: retinotopic mapping using deep learning
-----------------------------
---------------------------------------------------
Log files: /home/jovyan/workspace/books/examples
/functional_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260409_063529_output.
log and deepRetinotopy_20260409_063529_error.log
---------------------------------------------------
-----------------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovya
n/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-def
ormed_to-fsaverage template surfaces: /home/jovyan/workspace/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...
Processing single subject: sub-wlsubj001
Hemisphere: lh
Processing single subject: sub-wlsubj006
Out
put 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
-wlsubj006
=== Processing Step 1 for subject: sub-wlsubj006 ===
[sub-wlsubj006] Using FreeSurfer dir
ectory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfe
r/sub-wlsubj006/surf
[sub-wlsubj006] Fast mode enabled.
[sub-wlsubj006] [Step 1.1] Generating mid-thickness surface and c
urvature data if not available...
[sub-wlsubj006] Converting surfaces...
Processing subject: sub-wlsubj007
=== Processing Step 1 for subject: sub-wlsubj007 ===
[sub-wlsubj00
7] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj007/surf
Log files location: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivativ
es/freesurfer/logs
Output log: deepRetinotopy_20260409_063530_output.log
Error log: deepRetinotopy_2
0260409_063530_error.log
---------------------------------------------------------------------------
-----
DeepRetinotopy: retinotopic mapping using deep learning
--------------------------------------
------------------------------------------
Log files: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/logs/deepRetinotopy_20260409_063530_output.log and d
eepRetinotopy_20260409_063530_error.log
------------------------------------------------------------
--------------------
Directories and parameters:

Path to FreeSurfer directory: /home/jovyan/workspa
ce/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
Path to fs_LR-deformed_to-
fsaverage template surfaces: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/
templates
Dataset name: nyu
Maps: polarAngle eccentricity
Processing mode: Single subject (sub-wlsub
j001)
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...
[sub-wlsubj007] Fast mode enabled.
[sub-wlsubj007] [Step 1.1] Generating mid-thickness surface and c
urvature data if not available...
[sub-wlsubj007] Converting surfaces...
Hemisphere: lh
Processing single subject: sub-wlsubj001
Output mode: In-place (within FreeSurfer dir
ectory structure)
Hemisphere: lh
Processing single subject: sub-wlsubj004
Output mode: In-place (within FreeSurfer dir
ectory structure)
Processing subject: sub-wlsubj001
=== Processing Step 1 for subject: sub-wlsubj001 ===
[sub-wlsubj00
1] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj001/surf
[sub-wlsubj001] Fast mode enabled.
[sub-wlsubj001] [Step 1.1] Generating mid-thickness surface and c
urvature data if not available...
[sub-wlsubj001] Mid-thickness surface and curvature data already a
vailable
[sub-wlsubj001] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj001] Resampled curvature data already available
Processing subject: sub-wlsubj004
=== Processing Step 1 for subject: sub-wlsubj004 ===
[sub-wlsubj00
4] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj004/surf
[sub-wlsubj004] Fast mode enabled.
[sub-wlsubj004] [Step 1.1] Generating mid-thickness surface and c
urvature data if not available...
[sub-wlsubj004] Converting surfaces...
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 1s
Subject processed: sub-wlsubj001
Output location: In-place within FreeSurfer directory
=============
==================================
--------------------------------------------------------------------------------
Map: polarAngle
---
-----------------------------------------------------------------------------
[Step 2] Retinotopy prediction...
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj006/surf/lh.white.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/lh.white.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/lh.white.gii as a surface
Saving /home/jovyan/workspace/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/workspace/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/workspace/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/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj006/surf/lh.graymid.gii
Midthickness surface saved at /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj007/surf/lh.graymid.gii
Midthickness surface saved at /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj004/surf/lh.graymid.gii
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj006/surf/lh.graymid as a surface
[sub-wlsubj006] Computing curvature...
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/lh.graymid as a surface
[sub-wlsubj007] Computing curvature...
Saving /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj006/surf/lh.midthickness.surf.gii.temp37671.white.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/lh.midthickness.surf.gii.temp37686.white.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj006/surf/lh.midthickness.surf.gii.temp37671.pial.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/lh.midthickness.surf.gii.temp37800.white.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/lh.midthickness.surf.gii.temp37686.pial.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/lh.midthickness.surf.gii.temp37800.pial.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj006/surf/lh.sphere.reg.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/lh.sphere.reg.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/lh.sphere.reg.surf.gii as a surface
[sub-wlsubj007] Converting curvature data...
[sub-wlsubj006] Converting curvature data...
[sub-wlsubj004] Converting curvature data...
[sub-wlsubj007] Resampling native data to fsaverage space...
[sub-wlsubj006] Resampling native data to fsaverage space...
[sub-wlsubj004] Resampling native data to fsaverage space...
[sub-wlsubj007] Data resampling complete
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 33s
Su
bject processed: sub-wlsubj007
Output location: In-place within FreeSurfer directory
===============
================================
--------------------------------------------------------------------------------
Map: polarAngle
---
-----------------------------------------------------------------------------
[Step 2] Retinotopy pr
ediction...
[sub-wlsubj006] Data resampling complete
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 34s
Su
bject processed: sub-wlsubj006
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 38s
Su
bject processed: sub-wlsubj004
Output location: In-place within FreeSurfer directory
===============
================================
--------------------------------------------------------------------------------
Map: polarAngle
---
-----------------------------------------------------------------------------
[Step 2] Retinotopy pr
ediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAn
gle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer director
y structure)
===============================================
Output directory not specified, using i
nput path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesu
rfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/f
reesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/da
ta/ds003787/derivatives/freesurfer/processed_37480_714b0a65_47698
Processing single subject: sub-wls
ubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subject
s: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading t
ime: 0.48 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 mo
del 1...
Inference completed in 0.76 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Sa
ving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivati
ves/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing com
pleted in 0.80 minutes

===============================================
[Step 2] COMPLETED!
Total ex
ecution time: 1m 16s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: lh |
 Dataset: nyu
Output location: In-place within FreeSurfer directory
================================
===============
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_ima
ging/data/ds003787/derivatives/freesurfer/processed_37480_714b0a65_47698
[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: /ho
me/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsub
j001/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 24s
Su
bject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: lh
Output location: In-p
lace within FreeSurfer directory
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------
------------------------------
---------------------------------------------------------------------
-----------
Map: eccentricity
----------------------------------------------------------------------
----------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAn
gle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer director
y structure)
===============================================
Output directory not specified, using i
nput path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesu
rfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/f
reesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/da
ta/ds003787/derivatives/freesurfer/processed_38131_0fd9b710_75311
Processing single subject: sub-wls
ubj007
Found 1 subjects to process: ['sub-wlsubj007']
Final subject list after validation: 1 subject
s: ['sub-wlsubj007']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading t
ime: 0.52 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 mo
del 1...
Inference completed in 0.91 minutes
Saving predictions for 1 subjects...
[sub-wlsubj007] Sa
ving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivati
ves/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Created output directory
[sub-wlsubj007]
 Completed in 0.1s
Model 1 processing completed in 0.98 minutes

===================================
============
[Step 2] COMPLETED!
Total execution time: 1m 29s
Subject processed: sub-wlsubj007
Predi
ction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer d
irectory
===============================================
Cleaned up temporary directory: /home/jovya
n/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38131_0
fd9b710_75311
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAn
gle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer director
y structure)
===============================================
Output directory not specified, using i
nput path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesu
rfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/f
reesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/da
ta/ds003787/derivatives/freesurfer/processed_38166_107cabc9_76348
Processing single subject: sub-wls
ubj006
Found 1 subjects to process: ['sub-wlsubj006']
Final subject list after validation: 1 subject
s: ['sub-wlsubj006']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading t
ime: 0.52 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 mo
del 1...
Inference completed in 0.90 minutes
Saving predictions for 1 subjects...
[sub-wlsubj006] Sa
ving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivati
ves/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Created output directory
[sub-wlsubj006]
 Completed in 0.0s
Model 1 processing completed in 0.99 minutes

===================================
============
[Step 2] COMPLETED!
Total execution time: 1m 30s
Subject processed: sub-wlsubj006
Predi
ction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer d
irectory
===============================================
Cleaned up temporary directory: /home/jovya
n/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38166_1
07cabc9_76348
[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: /ho
me/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsub
j007/deepRetinotopy
[sub-wlsubj007] 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-wlsubj006
Output mode: In
-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj006
=== Processing Step 3 for subject: sub-wlsubj006 ===
[sub-wlsubj00
6] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Resampling ROI from fsaverage to native space for the left hemisphere...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAn
gle
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer director
y structure)
===============================================
Output directory not specified, using i
nput path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesu
rfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/f
reesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/da
ta/ds003787/derivatives/freesurfer/processed_38238_7418efef_78772
Processing single subject: sub-wls
ubj004
Found 1 subjects to process: ['sub-wlsubj004']
Final subject list after validation: 1 subject
s: ['sub-wlsubj004']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading t
ime: 0.56 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 mo
del 1...
Inference completed in 0.85 minutes
Saving predictions for 1 subjects...
[sub-wlsubj004] Sa
ving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivati
ves/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Created output directory
[sub-wlsubj004]
 Completed in 0.0s
Model 1 processing completed in 0.95 minutes

===================================
============
[Step 2] COMPLETED!
Total execution time: 1m 30s
Subject processed: sub-wlsubj004
Predi
ction type: polarAngle | Hemisphere: lh | Dataset: nyu
Output location: In-place within FreeSurfer d
irectory
===============================================
Cleaned up temporary directory: /home/jovya
n/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/processed_38238_7
418efef_78772
[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-wlsubj00
4] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Resampling ROI from fsaverage to native space for the left hemisphere...
[sub-wlsubj007] Resampling predicted map from fsaverage to native space for the left hemisphere...
[sub-wlsubj006] 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-wlsubj007] Transforming polar angle map of the left hemisphere...
[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 14s
Su
bject processed: sub-wlsubj007
Map: polarAngle | Model: model | Hemisphere: lh
Output location: In-p
lace within FreeSurfer directory
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------
------------------------------
---------------------------------------------------------------------
-----------
Map: eccentricity
----------------------------------------------------------------------
----------
[Step 2] Retinotopy prediction...
[sub-wlsubj006] Transforming polar angle map of the left hemisphere...
[sub-wlsubj006] Applying mask to the predicted map of the left hemisphere...
[sub-wlsubj004] Transforming polar angle map of the left hemisphere...
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 16s
Su
bject processed: sub-wlsubj006
Map: polarAngle | Model: model | Hemisphere: lh
Output location: In-p
lace within FreeSurfer directory
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------
------------------------------
---------------------------------------------------------------------
-----------
Map: eccentricity
----------------------------------------------------------------------
----------
[Step 2] Retinotopy prediction...
[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 15s
Su
bject processed: sub-wlsubj004
Map: polarAngle | Model: model | Hemisphere: lh
Output location: In-p
lace within FreeSurfer directory
===============================================
polarAngle resampling completed for lh hemisphere
--------------------------------------------------
------------------------------
---------------------------------------------------------------------
-----------
Map: eccentricity
----------------------------------------------------------------------
----------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentr
icity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer direct
ory structure)
===============================================
Output directory not specified, using
 input path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives
/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/
data/ds003787/derivatives/freesurfer/processed_38780_65af0339_82358
Processing single subject: sub-w
lsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subje
cts: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading
 time: 0.40 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 fo
r model 1...
Inference completed in 0.88 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001
] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deri
vatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing
 completed in 0.92 minutes

===============================================
[Step 2] COMPLETED!
Tota
l execution time: 1m 19s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere
: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
==========================
=====================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/processed_38780_65af0339_82358
[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-wlsubj00
1] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/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...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentr
icity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer direct
ory structure)
===============================================
Output directory not specified, using
 input path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives
/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/
data/ds003787/derivatives/freesurfer/processed_39195_9b26a987_93185
Processing single subject: sub-w
lsubj007
Found 1 subjects to process: ['sub-wlsubj007']
Final subject list after validation: 1 subje
cts: ['sub-wlsubj007']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading
 time: 0.46 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 fo
r model 1...
Inference completed in 0.95 minutes
Saving predictions for 1 subjects...
[sub-wlsubj007
] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deri
vatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Completed in 0.0s
Model 1 processing
 completed in 1.00 minutes

===============================================
[Step 2] COMPLETED!
Tota
l execution time: 1m 28s
Subject processed: sub-wlsubj007
Prediction type: eccentricity | Hemisphere
: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
==========================
=====================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/processed_39195_9b26a987_93185
[sub-wlsubj001] Applying mask to the predicted map of the left hemisphere...
[Step 3] Resampling predictions to native space...
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 19s
Su
bject processed: sub-wlsubj001
Map: eccentricity | Model: model | Hemisphere: lh
Output location: In
-place within FreeSurfer directory
===============================================
eccentricity resa
mpling completed for lh hemisphere
-----------------------------------------------------------------
---------------
Processing right hemisphere
--------------------------------------------------------
------------------------
[Step 1] Generating mid-thickness surface and curvature data...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentr
icity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer direct
ory structure)
===============================================
Output directory not specified, using
 input path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives
/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/
data/ds003787/derivatives/freesurfer/processed_39306_92a01df3_93871
Processing single subject: sub-w
lsubj006
Found 1 subjects to process: ['sub-wlsubj006']
Final subject list after validation: 1 subje
cts: ['sub-wlsubj006']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading
 time: 0.60 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 fo
r model 1...
Inference completed in 0.84 minutes
Saving predictions for 1 subjects...
[sub-wlsubj006
] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deri
vatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Completed in 0.0s
Model 1 processing
 completed in 0.90 minutes

===============================================
[Step 2] COMPLETED!
Tota
l execution time: 1m 30s
Subject processed: sub-wlsubj006
Prediction type: eccentricity | Hemisphere
: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
==========================
=====================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/processed_39306_92a01df3_93871
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-wlsubj00
1] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj001/surf
[sub-wlsubj001] Fast mode enabled.
[sub-wlsubj001] [Step 1.1] Generating mid-thickness surface and c
urvature data if not available...
[sub-wlsubj001] Mid-thickness surface and curvature data already a
vailable
[sub-wlsubj001] [Step 1.2] Preparing native surfaces for resampling...
[sub-wlsubj001] Resa
mpled curvature data already available
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-wlsubj00
7] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
=== Subject sub-wlsubj001 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 1s
Sub
ject processed: sub-wlsubj001
Output location: In-place within FreeSurfer directory
================
===============================
--------------------------------------------------------------------------------
Map: polarAngle
---
-----------------------------------------------------------------------------
[Step 2] Retinotopy pr
ediction...
[sub-wlsubj007] Resampling ROI from fsaverage to native space for the left hemisphere...
[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-wlsubj00
6] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Resampling ROI from fsaverage to native space for the left hemisphere...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentr
icity
Hemisphere: lh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer direct
ory structure)
===============================================
Output directory not specified, using
 input path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives
/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/
data/ds003787/derivatives/freesurfer/processed_39315_05989239_95591
Processing single subject: sub-w
lsubj004
Found 1 subjects to process: ['sub-wlsubj004']
Final subject list after validation: 1 subje
cts: ['sub-wlsubj004']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading
 time: 0.56 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 fo
r model 1...
Inference completed in 0.96 minutes
Saving predictions for 1 subjects...
[sub-wlsubj004
] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deri
vatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Completed in 0.0s
Model 1 processing
 completed in 1.02 minutes

===============================================
[Step 2] COMPLETED!
Tota
l execution time: 1m 34s
Subject processed: sub-wlsubj004
Prediction type: eccentricity | Hemisphere
: lh | Dataset: nyu
Output location: In-place within FreeSurfer directory
==========================
=====================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/processed_39315_05989239_95591
[sub-wlsubj007] Resampling predicted map from fsaverage to native space for the left hemisphere...
[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: /ho
me/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsub
j004/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] Applying mask to the predicted map of the left hemisphere...
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 14s
Su
bject 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 da
ta...
Hemisphere: rh
Processing single subject: sub-wlsubj007
Output mode: In-place (within FreeSurfer dir
ectory structure)
Processing subject: sub-wlsubj007
=== Processing Step 1 for subject: sub-wlsubj007 ===
[sub-wlsubj00
7] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj007/surf
[sub-wlsubj004] Resampling predicted map from fsaverage to native space for the left hemisphere...
[sub-wlsubj007] Fast mode enabled.
[sub-wlsubj007] [Step 1.1] Generating mid-thickness surface and c
urvature data if not available...
[sub-wlsubj007] Converting surfaces...
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/rh.white.gii as a surface
[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 17s
Su
bject processed: sub-wlsubj006
Map: eccentricity | Model: model | Hemisphere: lh
Output location: In
-place within FreeSurfer directory
===============================================
eccentricity resa
mpling 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 dir
ectory structure)
Processing subject: sub-wlsubj006
=== Processing Step 1 for subject: sub-wlsubj006 ===
[sub-wlsubj00
6] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj006/surf
[sub-wlsubj006] Fast mode enabled.
[sub-wlsubj006] [Step 1.1] Generating mid-thickness surface and c
urvature data if not available...
[sub-wlsubj006] 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 15s
Su
bject 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 da
ta...
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/rh.pial.gii as a surface
[sub-wlsubj007] Generating midthickness surface...
Hemisphere: rh
Processing single subject: sub-wlsubj004
Output mode: In-place (within FreeSurfer dir
ectory structure)
Processing subject: sub-wlsubj004
=== Processing Step 1 for subject: sub-wlsubj004 ===
[sub-wlsubj00
4] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj004/surf
[sub-wlsubj004] Fast mode enabled.
[sub-wlsubj004] [Step 1.1] Generating mid-thickness surface and c
urvature data if not available...
[sub-wlsubj004] Converting surfaces...
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj006/surf/rh.white.gii as a surface
Midthickness surface saved at /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj007/surf/rh.graymid.gii
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/rh.white.gii as a surface
Saving /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/rh.graymid as a surface
[sub-wlsubj007] Computing curvature...
Midthickness surface saved at /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj006/surf/rh.graymid.gii
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/rh.pial.gii as a surface
[sub-wlsubj004] Generating midthickness surface...
[sub-wlsubj007] Mid-thickness surface has been generated
[sub-wlsubj007] [Step 1.2] Preparing native
 surfaces for resampling...
[sub-wlsubj007] Running freesurfer-resample-prep...
Saving /home/jovyan/workspace/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/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj004/surf/rh.graymid.gii
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/rh.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...
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/rh.midthickness.surf.gii.temp40403.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/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/rh.midthickness.surf.gii.temp40403.pial.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj006/surf/rh.midthickness.surf.gii.temp40474.white.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj007/surf/rh.sphere.reg.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj006/surf/rh.midthickness.surf.gii.temp40474.pial.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/rh.midthickness.surf.gii.temp40536.white.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj006/surf/rh.sphere.reg.surf.gii as a surface
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/rh.midthickness.surf.gii.temp40536.pial.surf.gii as a surface
[sub-wlsubj007] Converting curvature data...
[sub-wlsubj007] Resampling native data to fsaverage space...
Saving /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer
/sub-wlsubj004/surf/rh.sphere.reg.surf.gii as a surface
[sub-wlsubj006] Converting curvature data...
[sub-wlsubj006] Resampling native data to fsaverage space...
[sub-wlsubj007] Data resampling complete
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 32s
Su
bject processed: sub-wlsubj007
Output location: In-place within FreeSurfer directory
===============
================================
--------------------------------------------------------------------------------
Map: polarAngle
---
-----------------------------------------------------------------------------
[Step 2] Retinotopy pr
ediction...
[sub-wlsubj004] Converting curvature data...
[sub-wlsubj006] Data resampling complete
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 32s
Su
bject processed: sub-wlsubj006
Output location: In-place within FreeSurfer directory
===============
================================
--------------------------------------------------------------------------------
Map: polarAngle
---
-----------------------------------------------------------------------------
[Step 2] Retinotopy pr
ediction...
[sub-wlsubj004] Resampling native data to fsaverage space...
[sub-wlsubj004] Data resampling complete
=== Subject sub-wlsubj004 completed in 0 minutes ===

===============================================
[Step 1] COMPLETED!
Total execution time: 0m 41s
Su
bject processed: sub-wlsubj004
Output location: In-place within FreeSurfer directory
===============
================================
-------------------------------------------------------------------
-------------
Map: polarAngle
----------------------------------------------------------------------
----------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAn
gle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer director
y structure)
===============================================
Output directory not specified, using i
nput path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesu
rfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/f
reesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/da
ta/ds003787/derivatives/freesurfer/processed_39903_bb8564f4_10103
Processing single subject: sub-wls
ubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subject
s: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading t
ime: 0.47 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 mo
del 1...
Inference completed in 0.58 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001] Sa
ving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivati
ves/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing com
pleted in 0.63 minutes

===============================================
[Step 2] COMPLETED!
Total ex
ecution time: 1m 6s
Subject processed: sub-wlsubj001
Prediction type: polarAngle | Hemisphere: rh |
Dataset: nyu
Output location: In-place within FreeSurfer directory
=================================
==============
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_imag
ing/data/ds003787/derivatives/freesurfer/processed_39903_bb8564f4_10103
[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-wlsubj00
1] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/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...
[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 21s
Su
bject processed: sub-wlsubj001
Map: polarAngle | Model: model | Hemisphere: rh
Output location: In-p
lace within FreeSurfer directory
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------
------------------------------
---------------------------------------------------------------------
-----------
Map: eccentricity
----------------------------------------------------------------------
----------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAn
gle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer director
y structure)
===============================================
Output directory not specified, using i
nput path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesu
rfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/f
reesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/da
ta/ds003787/derivatives/freesurfer/processed_40813_7309dffe_53404
Processing single subject: sub-wls
ubj007
Found 1 subjects to process: ['sub-wlsubj007']
Final subject list after validation: 1 subject
s: ['sub-wlsubj007']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading t
ime: 0.51 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 mo
del 1...
Inference completed in 0.95 minutes
Saving predictions for 1 subjects...
[sub-wlsubj007] Sa
ving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivati
ves/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Completed in 0.0s
Model 1 processing com
pleted in 1.00 minutes

===============================================
[Step 2] COMPLETED!
Total ex
ecution time: 1m 30s
Subject processed: sub-wlsubj007
Prediction type: polarAngle | Hemisphere: rh |
 Dataset: nyu
Output location: In-place within FreeSurfer directory
================================
===============
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_ima
ging/data/ds003787/derivatives/freesurfer/processed_40813_7309dffe_53404
[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: /ho
me/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsub
j007/deepRetinotopy
[sub-wlsubj007] Resampling ROI from fsaverage to native space for the right hemisphere...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAn
gle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer director
y structure)
===============================================
Output directory not specified, using i
nput path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesu
rfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/f
reesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/da
ta/ds003787/derivatives/freesurfer/processed_40926_62643bb6_57532
Processing single subject: sub-wls
ubj006
Found 1 subjects to process: ['sub-wlsubj006']
Final subject list after validation: 1 subject
s: ['sub-wlsubj006']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading t
ime: 0.65 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 mo
del 1...
Inference completed in 0.87 minutes
Saving predictions for 1 subjects...
[sub-wlsubj006] Sa
ving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivati
ves/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Completed in 0.0s
Model 1 processing com
pleted in 0.91 minutes

===============================================
[Step 2] COMPLETED!
Total ex
ecution time: 1m 33s
Subject processed: sub-wlsubj006
Prediction type: polarAngle | Hemisphere: rh |
 Dataset: nyu
Output location: In-place within FreeSurfer directory
================================
===============
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_ima
ging/data/ds003787/derivatives/freesurfer/processed_40926_62643bb6_57532
[Step 3] Resampling predictions to native space...
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-wlsubj00
6] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] 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-wlsubj007] Applying mask to the predicted map of the right hemisphere...
[sub-wlsubj006] Resampling predicted map from fsaverage to native space for the right hemisphere...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: polarAn
gle
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer director
y structure)
===============================================
Output directory not specified, using i
nput path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesu
rfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/f
reesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/da
ta/ds003787/derivatives/freesurfer/processed_41081_d581ea53_68045
Processing single subject: sub-wls
ubj004
Found 1 subjects to process: ['sub-wlsubj004']
Final subject list after validation: 1 subject
s: ['sub-wlsubj004']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading t
ime: 0.76 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 mo
del 1...
Inference completed in 0.82 minutes
Saving predictions for 1 subjects...
[sub-wlsubj004] Sa
ving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivati
ves/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Completed in 0.0s
Model 1 processing com
pleted in 0.88 minutes

===============================================
[Step 2] COMPLETED!
Total ex
ecution time: 1m 38s
Subject processed: sub-wlsubj004
Prediction type: polarAngle | Hemisphere: rh |
 Dataset: nyu
Output location: In-place within FreeSurfer directory
================================
===============
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/functional_ima
ging/data/ds003787/derivatives/freesurfer/processed_41081_d581ea53_68045
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 18s
Su
bject processed: sub-wlsubj007
Map: polarAngle | Model: model | Hemisphere: rh
Output location: In-p
lace within FreeSurfer directory
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------
------------------------------
---------------------------------------------------------------------
-----------
Map: eccentricity
----------------------------------------------------------------------
----------
[Step 2] Retinotopy prediction...
[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-wlsubj00
4] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj006] Applying mask to the predicted map of the right hemisphere...
=== Subject sub-wlsubj006 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 17s
Su
bject processed: sub-wlsubj006
Map: polarAngle | Model: model | Hemisphere: rh
Output location: In-p
lace within FreeSurfer directory
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------
------------------------------
--------------------------------------------------------------------------------
Map: eccentricity
-
-------------------------------------------------------------------------------
[Step 2] Retinotopy
prediction...
[sub-wlsubj004] 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 16s
Su
bject processed: sub-wlsubj004
Map: polarAngle | Model: model | Hemisphere: rh
Output location: In-p
lace within FreeSurfer directory
===============================================
polarAngle resampling completed for rh hemisphere
--------------------------------------------------
------------------------------
---------------------------------------------------------------------
-----------
Map: eccentricity
----------------------------------------------------------------------
----------
[Step 2] Retinotopy prediction...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentr
icity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer direct
ory structure)
===============================================
Output directory not specified, using
 input path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives
/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/
data/ds003787/derivatives/freesurfer/processed_41398_9ac10af5_33545
Processing single subject: sub-w
lsubj001
Found 1 subjects to process: ['sub-wlsubj001']
Final subject list after validation: 1 subje
cts: ['sub-wlsubj001']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading
 time: 0.76 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 fo
r model 1...
Inference completed in 0.59 minutes
Saving predictions for 1 subjects...
[sub-wlsubj001
] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deri
vatives/freesurfer/sub-wlsubj001/deepRetinotopy
[sub-wlsubj001] Completed in 0.0s
Model 1 processing
 completed in 0.65 minutes

===============================================
[Step 2] COMPLETED!
Tota
l execution time: 1m 24s
Subject processed: sub-wlsubj001
Prediction type: eccentricity | Hemisphere
: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
==========================
=====================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/processed_41398_9ac10af5_33545
[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: /ho
me/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/freesurfer/sub-wlsub
j001/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...
[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 22s
Su
bject 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: eccentr
icity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer direct
ory structure)
===============================================
Output directory not specified, using
 input path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives
/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/
data/ds003787/derivatives/freesurfer/processed_41902_938a3a7f_88250
Processing single subject: sub-w
lsubj006
Found 1 subjects to process: ['sub-wlsubj006']
Final subject list after validation: 1 subje
cts: ['sub-wlsubj006']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading
 time: 0.42 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 fo
r model 1...
Inference completed in 0.91 minutes
Saving predictions for 1 subjects...
[sub-wlsubj006
] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deri
vatives/freesurfer/sub-wlsubj006/deepRetinotopy
[sub-wlsubj006] Completed in 0.0s
Model 1 processing
 completed in 0.95 minutes

===============================================
[Step 2] COMPLETED!
Tota
l execution time: 1m 22s
Subject processed: sub-wlsubj006
Prediction type: eccentricity | Hemisphere
: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
==========================
=====================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/processed_41902_938a3a7f_88250
[Step 3] Resampling predictions to native space...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentr
icity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer direct
ory structure)
===============================================
Output directory not specified, using
 input path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives
/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/
data/ds003787/derivatives/freesurfer/processed_41771_f0ca39a3_88880
Processing single subject: sub-w
lsubj007
Found 1 subjects to process: ['sub-wlsubj007']
Final subject list after validation: 1 subje
cts: ['sub-wlsubj007']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading
 time: 0.55 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 fo
r model 1...
Inference completed in 0.83 minutes
Saving predictions for 1 subjects...
[sub-wlsubj007
] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deri
vatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] Completed in 0.0s
Model 1 processing
 completed in 0.88 minutes

===============================================
[Step 2] COMPLETED!
Tota
l execution time: 1m 25s
Subject processed: sub-wlsubj007
Prediction type: eccentricity | Hemisphere
: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
==========================
=====================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/processed_41771_f0ca39a3_88880
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-wlsubj00
6] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/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-wlsubj007
Output mode: In-place (within FreeSurfer directory structure)
Processing subject: sub-wlsubj007
=== Processing Step 3 for subject: sub-wlsubj007 ===
[sub-wlsubj00
7] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj007/deepRetinotopy
[sub-wlsubj007] 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-wlsubj006] Applying mask to the predicted map of the right hemisphere...
[sub-wlsubj007] Applying mask to the predicted map of the right hemisphere...
===============================================
[Step 2] STARTING INFERENCE
Prediction type: eccentr
icity
Hemisphere: rh
Dataset: nyu
Stimulus: original
Output mode: In-place (within FreeSurfer direct
ory structure)
===============================================
Output directory not specified, using
 input path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer
Data path: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives
/freesurfer
Temporary processed directory: /home/jovyan/workspace/books/examples/functional_imaging/
data/ds003787/derivatives/freesurfer/processed_42096_0001ef01_94984
Processing single subject: sub-w
lsubj004
Found 1 subjects to process: ['sub-wlsubj004']
Final subject list after validation: 1 subje
cts: ['sub-wlsubj004']
[Step 2.1] Loading the dataset...
Dataset loaded successfully
Dataset loading
 time: 0.71 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 fo
r model 1...
Inference completed in 0.80 minutes
Saving predictions for 1 subjects...
[sub-wlsubj004
] Saving predictions to: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deri
vatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Completed in 0.0s
Model 1 processing
 completed in 0.88 minutes

===============================================
[Step 2] COMPLETED!
Tota
l execution time: 1m 35s
Subject processed: sub-wlsubj004
Prediction type: eccentricity | Hemisphere
: rh | Dataset: nyu
Output location: In-place within FreeSurfer directory
==========================
=====================
Cleaned up temporary directory: /home/jovyan/workspace/books/examples/function
al_imaging/data/ds003787/derivatives/freesurfer/processed_42096_0001ef01_94984
=== Subject sub-wlsubj006 completed in 0 minutes ===
=== Subject sub-wlsubj007 completed in 0 minutes ===

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 16s
Su
bject processed: sub-wlsubj006
Map: eccentricity | Model: model | Hemisphere: rh
Output location: In
-place within FreeSurfer directory
===============================================
eccentricity resa
mpling completed for rh hemisphere
-----------------------------------------------------------------
---------------
Execution completed!

===============================================
[Step 3] COMPLETED!
Total execution time: 0m 15s
Su
bject processed: sub-wlsubj007
Map: eccentricity | Model: model | Hemisphere: rh
Output location: In
-place within FreeSurfer directory
===============================================
eccentricity resampling completed for rh hemisphere
------------------------------------------------
--------------------------------
Execution completed!
[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-wlsubj00
4] Using FreeSurfer directory: /home/jovyan/workspace/books/examples/functional_imaging/data/ds00378
7/derivatives/freesurfer/sub-wlsubj004/deepRetinotopy
[sub-wlsubj004] Resampling ROI from fsaverage to native space for the right hemisphere...
[sub-wlsubj004] 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 10s
Su
bject processed: sub-wlsubj004
Map: eccentricity | Model: model | Hemisphere: rh
Output location: In
-place within FreeSurfer directory
===============================================
eccentricity resa
mpling 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 iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.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/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj006/surf/lh.graymid.K...
done.
writing mean curvature to /home/jovyan/workspace/books/examples/functional_imaging/data/ds0037
87/derivatives/freesurfer/sub-wlsubj006/surf/lh.graymid.H...
done.
total integrated curvature = -0.559*4pi (-7.022) --> 2 handles
ICI = 144.8, FI = 1382.4, variation=22337.118
writing Gaussian curvature to /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj007/surf/lh.graymid.K...
done.
writing mean curvature to /home/jovyan/workspace/books/examples/functional_imaging/data/ds0037
87/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/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj004/surf/lh.graymid.K...
done.
writing mean curvature to /home/jovyan/workspace/books/examples/functional_imaging/data/ds0037
87/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 iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.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 iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.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 iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
Processing...
Processing...
Done!
Done!
Done!

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

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.lh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "

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

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

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

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj007/deepRetinotopy/sub-wlsubj007.ROI.lh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!
Processing...

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj006/deepRetinotopy/sub-wlsubj006.ROI.lh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj004/deepRetinotopy/sub-wlsubj004.ROI.lh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.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 iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.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 iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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'. "
Processing...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An is
sue 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/libpy
g.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_lh.label.gii con
tains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.lh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!

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

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

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj007/deepRetinotopy/sub-wlsubj007.ROI.lh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
WARNING
:
Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_lh.label.gii con
tains data array with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj006/deepRetinotopy/sub-wlsubj006.ROI.lh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj004/deepRetinotopy/sub-wlsubj004.ROI.lh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
Processing...
** 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/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj007/surf/rh.graymid.K...
done.
writing mean curvature to /home/jovyan/workspace/books/examples/functional_imaging/data/ds0037
87/derivatives/freesurfer/sub-wlsubj007/surf/rh.graymid.H...
done.
** DA[1] has coordsys with intent NIFTI_INTENT_TRIANGLE (should be NIFTI_INTENT_POINTSET)
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/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj006/surf/rh.graymid.K...
done.
writing mean curvature to /home/jovyan/workspace/books/examples/functional_imaging/data/ds0037
87/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/workspace/books/examples/functional_imaging/data/ds003787
/derivatives/freesurfer/sub-wlsubj004/surf/rh.graymid.K...
done.
writing mean curvature to /home/jovyan/workspace/books/examples/functional_imaging/data/ds0037
87/derivatives/freesurfer/sub-wlsubj004/surf/rh.graymid.H...
done.
Done!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.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 is
sue 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/libpy
g.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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'. "
Processing...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An is
sue 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/libpy
g.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
WARNING
:
Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii con
tains data array with NIFTI_INTENT_LABEL !!!
Done!

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.rh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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'. "
Done!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:124: UserWarning: An is
sue 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/libpy
g.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.lab
el.gii contains data array with NIFTI_INTENT_LABEL !!!
WARNING
:
Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer/sub-wlsubj007/deepRetinotopy/sub-wlsubj007.ROI.rh.native.label.gii contains data array with N
IFTI_INTENT_LABEL !!!

WARNING: Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.lab
el.gii contains data array with NIFTI_INTENT_LABEL !!!
WARNING
:
Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer/sub-wlsubj006/deepRetinotopy/sub-wlsubj006.ROI.rh.native.label.gii contains data array with N
IFTI_INTENT_LABEL !!!
WARNING
:
Metric File: /opt/deepRetinotopy_TheToolbox/main/../labels/ROI_WangPlusFovea/ROI.fs_rh.label.gii con
tains data array with NIFTI_INTENT_LABEL !!!
Done!
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.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 is
sue 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/libpy
g.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
WARNING
:
Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/derivatives/free
surfer/sub-wlsubj004/deepRetinotopy/sub-wlsubj004.ROI.rh.native.label.gii contains data array with N
IFTI_INTENT_LABEL !!!
Processing...
Processing...
/opt/miniconda-latest/lib/python3.12/site-packages/torch_geometric/typing.py:68: UserWarning: An iss
ue occurred while importing 'pyg-lib'. Disabling its usage. Stacktrace: /usr/lib64/libm.so.6: versio
n `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 is
sue 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/libpy
g.so)
  warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
Processing...
Done!
Done!

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

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj001/deepRetinotopy/sub-wlsubj001.ROI.rh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!

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

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

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj006/deepRetinotopy/sub-wlsubj006.ROI.rh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj007/deepRetinotopy/sub-wlsubj007.ROI.rh.native.label.gii contains data ar
ray with NIFTI_INTENT_LABEL !!!

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

WARNING: Metric File: /home/jovyan/workspace/books/examples/functional_imaging/data/ds003787/deriva
tives/freesurfer/sub-wlsubj004/deepRetinotopy/sub-wlsubj004.ROI.rh.native.label.gii contains data ar
ray 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

⚠️ Note: ipywidgets that rely on Python callbacks (observe, on_click) require a running kernel and do not function in the static HTML version of this notebook. Widgets using client-side trait linking (jslink) remain interactive without a kernel. 

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)

Dependencies in Jupyter/Python#

  • Using the package watermark to document system environment and software versions used in this notebook, alongside the Neurodesktop version extracted from the JUPYTER_IMAGE or NEURODESKTOP_VERSION environment variables.

import os

%load_ext watermark

%watermark
%watermark --iversions

neurodesktop_version = (
    os.environ.get('JUPYTER_IMAGE', '').split(':')[-1] or
    os.environ.get('NEURODESKTOP_VERSION', 'unknown')
)

print(f"Neurodesktop version: {neurodesktop_version}")

Last updated: 2026-04-09T06:45:06.290490+00:00

Python implementation: CPython
Python version       : 3.13.9
IPython version      : 9.7.0

Compiler    : GCC 14.3.0
OS          : Linux
Release     : 5.15.0-171-generic
Machine     : x86_64
Processor   : x86_64
CPU cores   : 32
Architecture: 64bit

IPython   : 9.7.0
ipywidgets: 7.8.5
nibabel   : 5.3.3
nilearn   : 0.13.1
numpy     : 2.3.5

Neurodesktop version: 2025-12-20