ASLprep#
Author: Steffen Bollmann
Setup Neurodesk#
%%capture
import os
import sys
IN_COLAB = 'google.colab' in sys.modules
if IN_COLAB:
os.environ["LD_PRELOAD"] = "";
os.environ["APPTAINER_BINDPATH"] = "/content,/tmp,/cvmfs"
os.environ["MPLCONFIGDIR"] = "/content/matplotlib-mpldir"
os.environ["LMOD_CMD"] = "/usr/share/lmod/lmod/libexec/lmod"
!curl -J -O https://raw.githubusercontent.com/NeuroDesk/neurocommand/main/googlecolab_setup.sh
!chmod +x googlecolab_setup.sh
!./googlecolab_setup.sh
os.environ["MODULEPATH"] = ':'.join(map(str, list(map(lambda x: os.path.join(os.path.abspath('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/'), x),os.listdir('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/')))))
# Output CPU information:
!cat /proc/cpuinfo | grep 'vendor' | uniq
!cat /proc/cpuinfo | grep 'model name' | uniq
vendor_id : AuthenticAMD
model name : AMD EPYC-Rome Processor
Run aslprep#
# load fmriprep
import lmod
import os
await lmod.load('aslprep/0.7.2')
await lmod.list()
['aslprep/0.7.2']
# Request a freesurfer license and store it in your homedirectory. This is just an exampe - 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 using datalad
!datalad install https://github.com/OpenNeuroDatasets/ds000240.git
!cd ds000240 && datalad get sub-01
Cloning: 0%| | 0.00/2.00 [00:00<?, ? candidates/s]
Enumerating: 0.00 Objects [00:00, ? Objects/s]
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Receiving: 0%| | 0.00/2.39k [00:00<?, ? Objects/s]
Resolving: 0%| | 0.00/256 [00:00<?, ? Deltas/s]
[INFO ] scanning for unlocked files (this may take some time)
[INFO ] Remote origin not usable by git-annex; setting annex-ignore
[INFO ] access to 1 dataset sibling s3-PRIVATE not auto-enabled, enable with:
| datalad siblings -d "/home/jovyan/example-notebooks/books/functional_imaging/ds000240" enable -s s3-PRIVATE
install(ok): /home/jovyan/example-notebooks/books/functional_imaging/ds000240 (dataset)
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get(ok): sub-01/anat/sub-01_T1w.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-01/perf/sub-01_asl.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-01 (directory)
action summary:
get (ok: 3)
%%bash
# aslprep data/bids_root/ out/ participant -w work/
aslprep ds000240 \
aslprep-output \
participant \
--participant-label 01 \
--fs-license-file ~/.license \
-w aslprep-work
bids-validator@1.14.5
This dataset appears to be BIDS compatible.
Summary: Available Tasks: Available Modalities:
133 Files, 17.76MB MRI
63 - Subjects
1 - Session
If you have any questions, please post on https://neurostars.org/tags/bids.
241015-23:33:33,303 nipype.workflow IMPORTANT:
Running ASLPrep version 0.7.2
License NOTICE ##################################################
ASLPrep 0.7.2
Copyright 2023 The PennLINC Team and the NiPreps Developers.
This product is primarily developed by the PennLINC team,
but it is also a part of the NiPreps community.
This product includes software developed by
the NiPreps Community (https://nipreps.org/).
Portions of this software were developed at the Department of
Psychology at Stanford University, Stanford, CA, US.
This software is also distributed as a Docker container image.
The bootstrapping file for the image ("Dockerfile") is licensed
under the MIT License.
This software may be distributed through an add-on package called
"Docker Wrapper" that is under the BSD 3-clause License.
#################################################################
241015-23:33:35,956 nipype.workflow IMPORTANT:
Building ASLPrep's workflow:
* BIDS dataset path: /home/jovyan/example-notebooks/books/functional_imaging/ds000240.
* Participant list: ['01'].
* Run identifier: 20241015-233301_3bb07981-a206-4abb-a9aa-fb634e8f410d.
* Output spaces: MNI152NLin2009cAsym:res-native.
* Pre-run FreeSurfer's SUBJECTS_DIR: /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer.
241015-23:33:36,843 nipype.workflow INFO:
ANAT Stage 1: Adding template workflow
241015-23:33:37,795 nipype.workflow INFO:
ANAT Stage 2: Preparing brain extraction workflow
241015-23:33:37,992 nipype.workflow INFO:
ANAT Stage 3: Preparing segmentation workflow
241015-23:33:38,3 nipype.workflow INFO:
ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
241015-23:33:38,21 nipype.workflow INFO:
ANAT Stage 5: Preparing surface reconstruction workflow
241015-23:33:38,65 nipype.workflow INFO:
ANAT Stage 6: Preparing mask refinement workflow
241015-23:33:38,70 nipype.workflow INFO:
ANAT No T2w images provided - skipping Stage 7
241015-23:33:38,71 nipype.workflow INFO:
ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
241015-23:33:38,109 nipype.workflow INFO:
ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
241015-23:33:38,125 nipype.workflow INFO:
ANAT Stage 8a: Creating cortical ribbon mask
241015-23:33:38,136 nipype.workflow INFO:
ANAT Stage 9: Creating fsLR registration sphere
241015-23:33:38,148 nipype.workflow INFO:
ANAT Stage 10: MSM-Sulc disabled
241015-23:33:38,577 nipype.workflow INFO:
Collected run data for /home/jovyan/example-notebooks/books/functional_imaging/ds000240/sub-01/perf/sub-01_asl.nii.gz:
aslcontext: /home/jovyan/example-notebooks/books/functional_imaging/ds000240/sub-01/perf/sub-01_aslcontext.tsv
m0scan: null
sbref: null
241015-23:33:38,614 nipype.workflow INFO:
No single-band-reference found for sub-01_asl.nii.gz.
241015-23:33:38,829 nipype.workflow INFO:
Stage 1: Adding HMC aslref workflow
241015-23:33:38,845 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
241015-23:33:38,857 nipype.workflow INFO:
Stage 3: Adding coregistration aslref workflow
241015-23:33:46,466 nipype.workflow INFO:
ASLPrep workflow graph with 414 nodes built successfully.
241015-23:34:14,129 nipype.workflow IMPORTANT:
ASLPrep started!
241015-23:34:18,459 nipype.interface WARNING:
Cannot determine world direction of phase encoding. Orientation: RAS; PE dir: None
241015-23:34:23,642 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.full_wm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/full_wm".
241015-23:34:23,646 nipype.workflow INFO:
[Node] Executing "full_wm" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:23,907 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.res_tmpl" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/res_tmpl".
241015-23:34:23,910 nipype.workflow INFO:
[Node] Executing "res_tmpl" <niworkflows.interfaces.nibabel.RegridToZooms>
241015-23:34:24,16 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.processing_target" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/processing_target".
241015-23:34:24,18 nipype.workflow INFO:
[Node] Executing "processing_target" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:24,132 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.lap_tmpl" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/lap_tmpl".
241015-23:34:24,134 nipype.workflow INFO:
[Node] Executing "lap_tmpl" <nipype.interfaces.ants.utils.ImageMath>
241015-23:34:24,354 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.ds_hmc_aslref_wf.raw_sources" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/ds_hmc_aslref_wf/raw_sources".
241015-23:34:24,358 nipype.workflow INFO:
[Node] Executing "raw_sources" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:24,364 nipype.workflow INFO:
[Node] Finished "raw_sources", elapsed time 0.000742s.
241015-23:34:24,368 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.ds_hmc_wf.raw_sources" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/ds_hmc_wf/raw_sources".
241015-23:34:24,371 nipype.workflow INFO:
[Node] Executing "raw_sources" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:24,372 nipype.workflow INFO:
[Node] Finished "raw_sources", elapsed time 0.000636s.
241015-23:34:24,375 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_native_wf.processing_target" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_native_wf/processing_target".
241015-23:34:24,378 nipype.workflow INFO:
[Node] Executing "processing_target" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:24,513 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.hmc_aslref_wf.val_asl" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/hmc_aslref_wf/val_asl".
241015-23:34:24,516 nipype.workflow INFO:
[Node] Executing "val_asl" <niworkflows.interfaces.header.ValidateImage>
241015-23:34:24,626 nipype.workflow INFO:
[Node] Finished "val_asl", elapsed time 0.103679s.
241015-23:34:24,638 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.ds_asl_std_wf.raw_sources" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/ds_asl_std_wf/raw_sources".
241015-23:34:24,641 nipype.workflow INFO:
[Node] Executing "raw_sources" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:24,643 nipype.workflow INFO:
[Node] Finished "raw_sources", elapsed time 0.000873s.
241015-23:34:24,644 nipype.workflow INFO:
[Node] Finished "processing_target", elapsed time 0.620777s.
241015-23:34:24,658 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.parcellate_cbf_wf.atlas_name_grabber" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_name_grabber".
241015-23:34:24,661 nipype.workflow INFO:
[Node] Executing "atlas_name_grabber" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:24,662 nipype.workflow INFO:
[Node] Finished "atlas_name_grabber", elapsed time 0.000655s.
241015-23:34:25,9 nipype.workflow INFO:
[Node] Finished "processing_target", elapsed time 0.630156s.
241015-23:34:25,20 nipype.workflow INFO:
[Node] Finished "full_wm", elapsed time 1.367654s.
241015-23:34:25,68 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_native_wf.validate_asl" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_native_wf/validate_asl".
241015-23:34:25,70 nipype.workflow INFO:
[Node] Executing "validate_asl" <niworkflows.interfaces.header.ValidateImage>
241015-23:34:25,185 nipype.workflow INFO:
[Node] Finished "validate_asl", elapsed time 0.109683s.
241015-23:34:25,668 nipype.workflow INFO:
[Node] Finished "res_tmpl", elapsed time 1.751608s.
241015-23:34:27,873 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber0".
241015-23:34:27,876 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber1".
241015-23:34:27,878 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber2".
241015-23:34:27,878 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber0" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,879 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber3" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber3".
241015-23:34:27,880 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber1" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,880 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber4" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber4".
241015-23:34:27,882 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber2" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,882 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber5" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber5".
241015-23:34:27,883 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber3" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,883 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber6" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber6".
241015-23:34:27,885 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber4" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,886 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber5" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,886 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber6" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,889 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber3", elapsed time 0.004739s.
241015-23:34:27,891 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber1", elapsed time 0.004406s.
241015-23:34:27,893 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber7" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber7".
241015-23:34:27,894 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber6", elapsed time 0.006154s.
241015-23:34:27,894 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber2", elapsed time 0.006392s.
241015-23:34:27,896 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber8" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber8".
241015-23:34:27,896 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber7" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,897 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber9" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber9".
241015-23:34:27,898 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber8" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,900 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber9" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,903 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber4", elapsed time 0.011844s.
241015-23:34:27,903 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber5", elapsed time 0.009827s.
241015-23:34:27,904 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber8", elapsed time 0.004553s.
241015-23:34:27,904 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber7", elapsed time 0.006769s.
241015-23:34:27,904 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber9", elapsed time 0.003245s.
241015-23:34:27,904 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber10" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber10".
241015-23:34:27,904 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber0", elapsed time 0.025012s.
241015-23:34:27,907 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber11" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber11".
241015-23:34:27,907 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber12" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber12".
241015-23:34:27,908 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber13" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber13".
241015-23:34:27,909 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber11" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,909 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber12" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,910 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber13" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,910 nipype.workflow INFO:
[Node] Executing "_atlas_file_grabber10" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:27,911 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber11", elapsed time 0.001751s.
241015-23:34:27,912 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber12", elapsed time 0.00191s.
241015-23:34:27,913 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber13", elapsed time 0.001958s.
241015-23:34:27,914 nipype.workflow INFO:
[Node] Finished "_atlas_file_grabber10", elapsed time 0.002364s.
241015-23:34:28,832 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.bidssrc" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/bidssrc".
241015-23:34:28,835 nipype.workflow INFO:
[Node] Executing "bidssrc" <aslprep.interfaces.bids.BIDSDataGrabber>
241015-23:34:28,840 nipype.interface INFO:
No "t2w" images found for sub-01
241015-23:34:28,840 nipype.interface INFO:
No "flair" images found for sub-01
241015-23:34:28,840 nipype.interface INFO:
No "fmap" images found for sub-01
241015-23:34:28,840 nipype.interface INFO:
No "sbref" images found for sub-01
241015-23:34:28,841 nipype.interface INFO:
No "roi" images found for sub-01
241015-23:34:28,842 nipype.workflow INFO:
[Node] Finished "bidssrc", elapsed time 0.001041s.
241015-23:34:29,579 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.hmc_aslref_wf.select_highest_contrast_volumes" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/hmc_aslref_wf/select_highest_contrast_volumes".
241015-23:34:29,589 nipype.workflow INFO:
[Node] Executing "select_highest_contrast_volumes" <aslprep.interfaces.reference.SelectHighestContrastVolumes>
241015-23:34:29,657 nipype.interface INFO:
Selecting m0scan as highest-contrast volume type for reference volume generation.
241015-23:34:29,851 nipype.workflow INFO:
[Node] Finished "select_highest_contrast_volumes", elapsed time 0.261419s.
241015-23:34:30,165 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.anat_template_wf.anat_ref_dimensions" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/anat_template_wf/anat_ref_dimensions".
241015-23:34:30,374 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber0".
241015-23:34:30,375 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber0" - collecting precomputed outputs
241015-23:34:30,376 nipype.workflow INFO:
[Node] "_atlas_file_grabber0" found cached.
241015-23:34:30,377 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber1".
241015-23:34:30,378 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber1" - collecting precomputed outputs
241015-23:34:30,378 nipype.workflow INFO:
[Node] "_atlas_file_grabber1" found cached.
241015-23:34:30,380 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber2".
241015-23:34:30,381 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber2" - collecting precomputed outputs
241015-23:34:30,381 nipype.workflow INFO:
[Node] "_atlas_file_grabber2" found cached.
241015-23:34:30,382 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber3" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber3".
241015-23:34:30,383 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber3" - collecting precomputed outputs
241015-23:34:30,383 nipype.workflow INFO:
[Node] "_atlas_file_grabber3" found cached.
241015-23:34:30,385 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber4" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber4".
241015-23:34:30,386 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber4" - collecting precomputed outputs
241015-23:34:30,386 nipype.workflow INFO:
[Node] "_atlas_file_grabber4" found cached.
241015-23:34:30,387 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber5" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber5".
241015-23:34:30,388 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber5" - collecting precomputed outputs
241015-23:34:30,388 nipype.workflow INFO:
[Node] "_atlas_file_grabber5" found cached.
241015-23:34:30,389 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber6" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber6".
241015-23:34:30,390 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber6" - collecting precomputed outputs
241015-23:34:30,390 nipype.workflow INFO:
[Node] "_atlas_file_grabber6" found cached.
241015-23:34:30,392 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber7" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber7".
241015-23:34:30,393 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber7" - collecting precomputed outputs
241015-23:34:30,393 nipype.workflow INFO:
[Node] "_atlas_file_grabber7" found cached.
241015-23:34:30,394 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber8" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber8".
241015-23:34:30,395 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber8" - collecting precomputed outputs
241015-23:34:30,395 nipype.workflow INFO:
[Node] "_atlas_file_grabber8" found cached.
241015-23:34:30,396 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber9" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber9".
241015-23:34:30,397 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber9" - collecting precomputed outputs
241015-23:34:30,397 nipype.workflow INFO:
[Node] "_atlas_file_grabber9" found cached.
241015-23:34:30,398 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber10" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber10".
241015-23:34:30,399 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber10" - collecting precomputed outputs
241015-23:34:30,400 nipype.workflow INFO:
[Node] "_atlas_file_grabber10" found cached.
241015-23:34:30,401 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber11" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber11".
241015-23:34:30,402 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber11" - collecting precomputed outputs
241015-23:34:30,402 nipype.workflow INFO:
[Node] "_atlas_file_grabber11" found cached.
241015-23:34:30,403 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber12" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber12".
241015-23:34:30,404 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber12" - collecting precomputed outputs
241015-23:34:30,404 nipype.workflow INFO:
[Node] "_atlas_file_grabber12" found cached.
241015-23:34:30,406 nipype.workflow INFO:
[Node] Setting-up "_atlas_file_grabber13" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/atlas_file_grabber/mapflow/_atlas_file_grabber13".
241015-23:34:30,407 nipype.workflow INFO:
[Node] Cached "_atlas_file_grabber13" - collecting precomputed outputs
241015-23:34:30,407 nipype.workflow INFO:
[Node] "_atlas_file_grabber13" found cached.
241015-23:34:30,602 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.reduce_asl_file" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/reduce_asl_file".
241015-23:34:30,608 nipype.workflow INFO:
[Node] Executing "reduce_asl_file" <aslprep.interfaces.utility.ReduceASLFiles>
241015-23:34:31,756 nipype.workflow INFO:
[Node] Finished "reduce_asl_file", elapsed time 1.146737s.
241015-23:34:31,811 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_native_wf.reduce_asl_file" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_native_wf/reduce_asl_file".
241015-23:34:31,835 nipype.workflow INFO:
[Node] Executing "reduce_asl_file" <aslprep.interfaces.utility.ReduceASLFiles>
241015-23:34:31,996 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.hmc_aslref_wf.gen_avg" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/hmc_aslref_wf/gen_avg".
241015-23:34:32,671 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.bids_info" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/bids_info".
241015-23:34:32,967 nipype.workflow INFO:
[Node] Finished "reduce_asl_file", elapsed time 1.130671s.
241015-23:34:33,985 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities0".
241015-23:34:33,987 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities1".
241015-23:34:33,987 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities2".
241015-23:34:33,988 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities0" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:33,989 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities3" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities3".
241015-23:34:33,990 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities0", elapsed time 0.001176s.
241015-23:34:33,990 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities1" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:33,990 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities4" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities4".
241015-23:34:33,991 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities2" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:33,992 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities5" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities5".
241015-23:34:33,993 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities6" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities6".
241015-23:34:33,993 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities1", elapsed time 0.001407s.
241015-23:34:33,993 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities3" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:33,994 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities4" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:33,994 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities2", elapsed time 0.001834s.
241015-23:34:33,995 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities5" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:33,995 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities7" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities7".
241015-23:34:33,996 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities6" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:33,996 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities9" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities9".
241015-23:34:33,996 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities3", elapsed time 0.001857s.
241015-23:34:33,996 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities4", elapsed time 0.001559s.
241015-23:34:33,997 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities8" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities8".
241015-23:34:33,997 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities5", elapsed time 0.001334s.
241015-23:34:33,998 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities7" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:33,998 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities9" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:34,0 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities8" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:34,0 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities9", elapsed time 0.001067s.
241015-23:34:34,1 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities7", elapsed time 0.001594s.
241015-23:34:34,1 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities10" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities10".
241015-23:34:34,3 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities6", elapsed time 0.001567s.
241015-23:34:34,4 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities13" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities13".
241015-23:34:34,4 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities12" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities12".
241015-23:34:34,4 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities11" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities11".
241015-23:34:34,5 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities10" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:34,6 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities8", elapsed time 0.001389s.
241015-23:34:34,6 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities13" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:34,7 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities11" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:34,7 nipype.workflow INFO:
[Node] Executing "_get_atlas_entities12" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:34,8 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities13", elapsed time 0.001059s.
241015-23:34:34,9 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities11", elapsed time 0.001382s.
241015-23:34:34,10 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities12", elapsed time 0.001622s.
241015-23:34:34,13 nipype.workflow INFO:
[Node] Finished "_get_atlas_entities10", elapsed time 0.001582s.
241015-23:34:35,964 nipype.workflow INFO:
[Node] Executing "anat_ref_dimensions" <niworkflows.interfaces.images.TemplateDimensions>
241015-23:34:36,35 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities0".
241015-23:34:36,36 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities0" - collecting precomputed outputs
241015-23:34:36,36 nipype.workflow INFO:
[Node] "_get_atlas_entities0" found cached.
241015-23:34:36,38 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities1".
241015-23:34:36,39 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities1" - collecting precomputed outputs
241015-23:34:36,39 nipype.workflow INFO:
[Node] "_get_atlas_entities1" found cached.
241015-23:34:36,41 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities2".
241015-23:34:36,42 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities2" - collecting precomputed outputs
241015-23:34:36,42 nipype.workflow INFO:
[Node] "_get_atlas_entities2" found cached.
241015-23:34:36,44 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities3" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities3".
241015-23:34:36,45 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities3" - collecting precomputed outputs
241015-23:34:36,45 nipype.workflow INFO:
[Node] "_get_atlas_entities3" found cached.
241015-23:34:36,47 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities4" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities4".
241015-23:34:36,48 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities4" - collecting precomputed outputs
241015-23:34:36,48 nipype.workflow INFO:
[Node] "_get_atlas_entities4" found cached.
241015-23:34:36,49 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities5" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities5".
241015-23:34:36,50 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities5" - collecting precomputed outputs
241015-23:34:36,50 nipype.workflow INFO:
[Node] "_get_atlas_entities5" found cached.
241015-23:34:36,52 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities6" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities6".
241015-23:34:36,53 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities6" - collecting precomputed outputs
241015-23:34:36,53 nipype.workflow INFO:
[Node] "_get_atlas_entities6" found cached.
241015-23:34:36,55 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities7" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities7".
241015-23:34:36,56 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities7" - collecting precomputed outputs
241015-23:34:36,57 nipype.workflow INFO:
[Node] "_get_atlas_entities7" found cached.
241015-23:34:36,59 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities8" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities8".
241015-23:34:36,60 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities8" - collecting precomputed outputs
241015-23:34:36,60 nipype.workflow INFO:
[Node] "_get_atlas_entities8" found cached.
241015-23:34:36,62 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities9" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities9".
241015-23:34:36,64 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities9" - collecting precomputed outputs
241015-23:34:36,64 nipype.workflow INFO:
[Node] "_get_atlas_entities9" found cached.
241015-23:34:36,65 nipype.workflow INFO:
[Node] Executing "bids_info" <niworkflows.interfaces.bids.BIDSInfo>
241015-23:34:36,66 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities10" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities10".
241015-23:34:36,67 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities10" - collecting precomputed outputs
241015-23:34:36,67 nipype.workflow INFO:
[Node] "_get_atlas_entities10" found cached.
241015-23:34:36,69 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities11" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities11".
241015-23:34:36,70 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities11" - collecting precomputed outputs
241015-23:34:36,70 nipype.workflow INFO:
[Node] "_get_atlas_entities11" found cached.
241015-23:34:36,70 nipype.workflow INFO:
[Node] Finished "bids_info", elapsed time 0.004438s.
241015-23:34:36,72 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities12" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities12".
241015-23:34:36,73 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities12" - collecting precomputed outputs
241015-23:34:36,73 nipype.workflow INFO:
[Node] "_get_atlas_entities12" found cached.
241015-23:34:36,75 nipype.workflow INFO:
[Node] Setting-up "_get_atlas_entities13" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/parcellate_cbf_wf/get_atlas_entities/mapflow/_get_atlas_entities13".
241015-23:34:36,76 nipype.workflow INFO:
[Node] Cached "_get_atlas_entities13" - collecting precomputed outputs
241015-23:34:36,76 nipype.workflow INFO:
[Node] "_get_atlas_entities13" found cached.
241015-23:34:36,653 nipype.workflow INFO:
[Node] Finished "anat_ref_dimensions", elapsed time 0.688146s.
241015-23:34:37,293 nipype.workflow INFO:
[Node] Finished "lap_tmpl", elapsed time 12.793348s.
241015-23:34:37,736 nipype.workflow INFO:
[Node] Executing "gen_avg" <niworkflows.interfaces.images.RobustAverage>
241015-23:34:37,992 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.mrg_tmpl" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/mrg_tmpl".
241015-23:34:37,998 nipype.workflow INFO:
[Node] Executing "mrg_tmpl" <nipype.interfaces.utility.base.Merge>
241015-23:34:37,999 nipype.workflow INFO:
[Node] Finished "mrg_tmpl", elapsed time 0.000406s.
241015-23:34:38,257 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.fs_isrunning" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/fs_isrunning".
241015-23:34:38,263 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.ds_t1w_mask_wf.raw_sources" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/ds_t1w_mask_wf/raw_sources".
241015-23:34:38,264 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.ds_ribbon_mask_wf.raw_sources" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/ds_ribbon_mask_wf/raw_sources".
241015-23:34:38,273 nipype.workflow INFO:
[Node] Setting-up "_denoise0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/_denoise0".
241015-23:34:38,276 nipype.workflow INFO:
[Node] Executing "_denoise0" <nipype.interfaces.ants.segmentation.DenoiseImage>
241015-23:34:38,494 nipype.interface INFO:
stderr 2024-10-15T23:34:38.493961:++ 3dvolreg: AFNI version=AFNI_24.1.08 (May 2 2024) [64-bit]
241015-23:34:38,494 nipype.interface INFO:
stderr 2024-10-15T23:34:38.493961:++ Authored by: RW Cox
241015-23:34:38,499 nipype.interface INFO:
stderr 2024-10-15T23:34:38.499782:** AFNI converts NIFTI_datatype=4 (INT16) in file /home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/hmc_aslref_wf/gen_avg/sub-01_asl_contrast_sliced.nii.gz to FLOAT32
241015-23:34:38,499 nipype.interface INFO:
stderr 2024-10-15T23:34:38.499782: Warnings of this type will be muted for this session.
241015-23:34:38,500 nipype.interface INFO:
stderr 2024-10-15T23:34:38.499782: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
241015-23:34:38,514 nipype.interface INFO:
stderr 2024-10-15T23:34:38.514547:++ Coarse del was 10, replaced with 2
241015-23:34:38,796 nipype.workflow INFO:
[Node] Executing "raw_sources" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:38,798 nipype.workflow INFO:
[Node] Finished "raw_sources", elapsed time 0.000885s.
241015-23:34:38,799 nipype.workflow INFO:
[Node] Executing "raw_sources" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:38,801 nipype.workflow INFO:
[Node] Finished "raw_sources", elapsed time 0.000814s.
241015-23:34:40,468 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S1056Parcels/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:40,732 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.asl_hmc_wf.split_by_volume_type" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/split_by_volume_type".
241015-23:34:40,737 nipype.workflow INFO:
[Node] Executing "split_by_volume_type" <aslprep.interfaces.utility.SplitByVolumeType>
241015-23:34:41,146 nipype.workflow INFO:
[Node] Executing "fs_isrunning" <nipype.interfaces.utility.wrappers.Function>
241015-23:34:41,149 nipype.workflow INFO:
[Node] Finished "fs_isrunning", elapsed time 0.001225s.
241015-23:34:41,947 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S156Parcels/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:42,403 nipype.workflow INFO:
[Node] Finished "split_by_volume_type", elapsed time 1.663437s.
241015-23:34:43,43 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S256Parcels/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:44,73 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S356Parcels/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:44,726 nipype.interface INFO:
stderr 2024-10-15T23:34:44.726188:++ Max displacement in automask = 0.96 (mm) at sub-brick 3
241015-23:34:44,726 nipype.interface INFO:
stderr 2024-10-15T23:34:44.726188:++ Max delta displ in automask = 0.93 (mm) at sub-brick 3
241015-23:34:45,106 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S456Parcels/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:45,362 nipype.workflow INFO:
[Node] Finished "gen_avg", elapsed time 7.6249590000000005s.
241015-23:34:46,275 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S556Parcels/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:48,55 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S656Parcels/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:49,99 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S756Parcels/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:50,112 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S856Parcels/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:51,156 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S956Parcels/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:34:52,237 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-Glasser/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz dtype from float32 to int16
241015-23:34:53,427 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-Gordon/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.nii.gz dtype from float32 to int16
241015-23:34:54,827 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-HCP/space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.nii.gz dtype from float32 to int16
241015-23:34:55,197 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-Tian/space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.nii.gz dtype from float32 to int16
241015-23:35:03,266 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.fmapref_buffer" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/fmapref_buffer".
241015-23:35:03,815 nipype.workflow INFO:
[Node] Executing "fmapref_buffer" <nipype.interfaces.utility.wrappers.Function>
241015-23:35:03,825 nipype.workflow INFO:
[Node] Finished "fmapref_buffer", elapsed time 0.00421s.
241015-23:35:03,840 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S1056Parcels/space-MNI152NLin6Asym_atlas-4S1056Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:05,295 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S156Parcels/space-MNI152NLin6Asym_atlas-4S156Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:06,270 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S256Parcels/space-MNI152NLin6Asym_atlas-4S256Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:07,353 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S356Parcels/space-MNI152NLin6Asym_atlas-4S356Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:08,851 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S456Parcels/space-MNI152NLin6Asym_atlas-4S456Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:10,246 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S556Parcels/space-MNI152NLin6Asym_atlas-4S556Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:11,658 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S656Parcels/space-MNI152NLin6Asym_atlas-4S656Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:13,23 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S756Parcels/space-MNI152NLin6Asym_atlas-4S756Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:13,865 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S856Parcels/space-MNI152NLin6Asym_atlas-4S856Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:14,678 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-4S956Parcels/space-MNI152NLin6Asym_atlas-4S956Parcels_res-01_dseg.nii.gz dtype from uint32 to int16
241015-23:35:15,508 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-Glasser/space-MNI152NLin6Asym_atlas-Glasser_res-01_dseg.nii.gz dtype from float32 to int16
241015-23:35:16,510 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-Gordon/space-MNI152NLin6Asym_atlas-Gordon_res-01_dseg.nii.gz dtype from float32 to int16
241015-23:35:17,665 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-HCP/space-MNI152NLin6Asym_atlas-HCP_res-02_dseg.nii.gz dtype from float32 to int16
241015-23:35:17,935 nipype.interface WARNING:
Changing /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/atlases/atlas-Tian/space-MNI152NLin6Asym_atlas-Tian_res-02_dseg.nii.gz dtype from float32 to int16
241015-23:35:19,718 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.ds_coreg_aslref_wf.raw_sources" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/ds_coreg_aslref_wf/raw_sources".
241015-23:35:19,722 nipype.workflow INFO:
[Node] Setting-up "_mcflirt2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/mcflirt/mapflow/_mcflirt2".
241015-23:35:19,730 nipype.workflow INFO:
[Node] Executing "_mcflirt2" <nipype.interfaces.fsl.preprocess.MCFLIRT>
241015-23:35:19,730 nipype.workflow INFO:
[Node] Executing "raw_sources" <nipype.interfaces.utility.wrappers.Function>
241015-23:35:19,732 nipype.workflow INFO:
[Node] Finished "raw_sources", elapsed time 0.000968s.
241015-23:35:20,118 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.init_aff" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/init_aff".
241015-23:35:20,123 nipype.workflow INFO:
[Node] Executing "init_aff" <nipype.interfaces.ants.utils.AI>
241015-23:35:20,177 nipype.workflow INFO:
[Node] Setting-up "_mcflirt0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/mcflirt/mapflow/_mcflirt0".
241015-23:35:20,181 nipype.workflow INFO:
[Node] Executing "_mcflirt0" <nipype.interfaces.fsl.preprocess.MCFLIRT>
241015-23:35:20,203 nipype.workflow INFO:
[Node] Setting-up "_mcflirt1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/mcflirt/mapflow/_mcflirt1".
241015-23:35:20,207 nipype.workflow INFO:
[Node] Executing "_mcflirt1" <nipype.interfaces.fsl.preprocess.MCFLIRT>
241015-23:35:22,658 nipype.workflow INFO:
[Node] Finished "_mcflirt2", elapsed time 2.926998s.
241015-23:35:23,676 nipype.workflow INFO:
[Node] Finished "_denoise0", elapsed time 44.818047s.
241015-23:35:25,770 nipype.workflow INFO:
[Node] Setting-up "_anat_conform0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/anat_template_wf/anat_conform/mapflow/_anat_conform0".
241015-23:35:25,772 nipype.workflow INFO:
[Node] Executing "_anat_conform0" <niworkflows.interfaces.images.Conform>
241015-23:35:28,45 nipype.workflow INFO:
[Node] Finished "_anat_conform0", elapsed time 2.272462s.
241015-23:35:28,368 nipype.workflow INFO:
[Node] Finished "_mcflirt1", elapsed time 8.155737s.
241015-23:35:29,722 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.anat_template_wf.get1st" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/anat_template_wf/get1st".
241015-23:35:29,725 nipype.workflow INFO:
[Node] Executing "get1st" <nipype.interfaces.utility.base.Select>
241015-23:35:29,726 nipype.workflow INFO:
[Node] Finished "get1st", elapsed time 0.00039s.
241015-23:35:33,410 nipype.workflow INFO:
[Node] Finished "_mcflirt0", elapsed time 13.227096s.
241015-23:35:34,898 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.fov_check" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/fov_check".
241015-23:35:34,902 nipype.workflow INFO:
[Node] Setting-up "_truncate_images0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0".
241015-23:35:34,905 nipype.workflow INFO:
[Node] Executing "_truncate_images0" <nipype.interfaces.ants.utils.ImageMath>
241015-23:35:34,929 nipype.workflow INFO:
[Node] Executing "fov_check" <nipype.interfaces.utility.wrappers.Function>
241015-23:35:35,33 nipype.workflow INFO:
[Node] Setting-up "_mcflirt0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/mcflirt/mapflow/_mcflirt0".
241015-23:35:35,41 nipype.workflow INFO:
[Node] Cached "_mcflirt0" - collecting precomputed outputs
241015-23:35:35,42 nipype.workflow INFO:
[Node] "_mcflirt0" found cached.
241015-23:35:35,44 nipype.workflow INFO:
[Node] Setting-up "_mcflirt1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/mcflirt/mapflow/_mcflirt1".
241015-23:35:35,50 nipype.workflow INFO:
[Node] Cached "_mcflirt1" - collecting precomputed outputs
241015-23:35:35,50 nipype.workflow INFO:
[Node] "_mcflirt1" found cached.
241015-23:35:35,52 nipype.workflow INFO:
[Node] Setting-up "_mcflirt2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/mcflirt/mapflow/_mcflirt2".
241015-23:35:35,55 nipype.workflow INFO:
[Node] Cached "_mcflirt2" - collecting precomputed outputs
241015-23:35:35,55 nipype.workflow INFO:
[Node] "_mcflirt2" found cached.
241015-23:35:35,474 nipype.workflow INFO:
[Node] Finished "fov_check", elapsed time 0.540739s.
241015-23:35:36,665 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.recon_config" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/recon_config".
241015-23:35:38,920 nipype.workflow INFO:
[Node] Setting-up "_listify_mat_files0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/listify_mat_files/mapflow/_listify_mat_files0".
241015-23:35:38,921 nipype.workflow INFO:
[Node] Setting-up "_listify_mat_files1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/listify_mat_files/mapflow/_listify_mat_files1".
241015-23:35:38,923 nipype.workflow INFO:
[Node] Setting-up "_listify_mat_files2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/listify_mat_files/mapflow/_listify_mat_files2".
241015-23:35:38,927 nipype.workflow INFO:
[Node] Executing "_listify_mat_files1" <nipype.interfaces.utility.wrappers.Function>
241015-23:35:38,928 nipype.workflow INFO:
[Node] Executing "_listify_mat_files2" <nipype.interfaces.utility.wrappers.Function>
241015-23:35:38,929 nipype.workflow INFO:
[Node] Finished "_listify_mat_files1", elapsed time 0.00056s.
241015-23:35:38,930 nipype.workflow INFO:
[Node] Finished "_listify_mat_files2", elapsed time 0.000796s.
241015-23:35:38,930 nipype.workflow INFO:
[Node] Executing "_listify_mat_files0" <nipype.interfaces.utility.wrappers.Function>
241015-23:35:38,932 nipype.workflow INFO:
[Node] Finished "_listify_mat_files0", elapsed time 0.000827s.
241015-23:35:40,918 nipype.workflow INFO:
[Node] Setting-up "_listify_mat_files0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/listify_mat_files/mapflow/_listify_mat_files0".
241015-23:35:40,923 nipype.workflow INFO:
[Node] Cached "_listify_mat_files0" - collecting precomputed outputs
241015-23:35:40,924 nipype.workflow INFO:
[Node] "_listify_mat_files0" found cached.
241015-23:35:40,925 nipype.workflow INFO:
[Node] Setting-up "_listify_mat_files1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/listify_mat_files/mapflow/_listify_mat_files1".
241015-23:35:40,930 nipype.workflow INFO:
[Node] Cached "_listify_mat_files1" - collecting precomputed outputs
241015-23:35:40,930 nipype.workflow INFO:
[Node] "_listify_mat_files1" found cached.
241015-23:35:40,931 nipype.workflow INFO:
[Node] Setting-up "_listify_mat_files2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/listify_mat_files/mapflow/_listify_mat_files2".
241015-23:35:40,933 nipype.workflow INFO:
[Node] Cached "_listify_mat_files2" - collecting precomputed outputs
241015-23:35:40,933 nipype.workflow INFO:
[Node] "_listify_mat_files2" found cached.
241015-23:35:41,577 nipype.workflow INFO:
[Node] Executing "recon_config" <niworkflows.interfaces.freesurfer.FSDetectInputs>
241015-23:35:41,650 nipype.workflow INFO:
[Node] Finished "recon_config", elapsed time 0.07135s.
241015-23:35:42,100 nipype.workflow INFO:
[Node] Finished "_truncate_images0", elapsed time 6.709567s.
241015-23:35:42,932 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.asl_hmc_wf.combine_motpars" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/combine_motpars".
241015-23:35:42,934 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon1".
241015-23:35:42,942 nipype.workflow INFO:
[Node] Setting-up "_inu_n40" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40".
241015-23:35:42,944 nipype.workflow INFO:
[Node] Executing "autorecon1" <smriprep.interfaces.freesurfer.ReconAll>
241015-23:35:42,945 nipype.workflow INFO:
[Node] Executing "_inu_n40" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
241015-23:35:42,951 nipype.workflow INFO:
[Node] Executing "combine_motpars" <aslprep.interfaces.utility.CombineMotionParameters>
241015-23:35:42,959 nipype.workflow INFO:
[Node] Finished "combine_motpars", elapsed time 0.007317s.
241015-23:35:44,922 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.asl_hmc_wf.normalize_motion" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/normalize_motion".
241015-23:35:44,922 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.asl_hmc_wf.rmsdiff" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/rmsdiff".
241015-23:35:44,937 nipype.workflow INFO:
[Node] Executing "normalize_motion" <aslprep.interfaces.confounds.NormalizeMotionParams>
241015-23:35:44,942 nipype.workflow INFO:
[Node] Finished "normalize_motion", elapsed time 0.003731s.
241015-23:35:44,966 nipype.workflow INFO:
[Node] Executing "rmsdiff" <aslprep.interfaces.utility.PairwiseRMSDiff>
241015-23:35:45,29 nipype.interface INFO:
stdout 2024-10-15T23:35:45.029529:0.0754411
241015-23:35:45,369 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.asl_hmc_wf.fsl2itk" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/asl_hmc_wf/fsl2itk".
241015-23:35:45,483 nipype.interface INFO:
stdout 2024-10-15T23:35:45.483757:0.0469867
241015-23:35:45,779 nipype.interface INFO:
stdout 2024-10-15T23:35:45.779630:0.268931
241015-23:35:46,95 nipype.interface INFO:
stdout 2024-10-15T23:35:46.095560:0.172064
241015-23:35:46,432 nipype.interface INFO:
stdout 2024-10-15T23:35:46.432704:0.229626
241015-23:35:46,750 nipype.interface INFO:
stdout 2024-10-15T23:35:46.750530:0.140681
241015-23:35:47,58 nipype.interface INFO:
stdout 2024-10-15T23:35:47.057960:0.0673405
241015-23:35:47,190 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_confounds_wf.fdisp" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_confounds_wf/fdisp".
241015-23:35:47,373 nipype.interface INFO:
stdout 2024-10-15T23:35:47.373088:0.106117
241015-23:35:47,702 nipype.interface INFO:
stdout 2024-10-15T23:35:47.702382:0.165799
241015-23:35:48,54 nipype.interface INFO:
stdout 2024-10-15T23:35:48.054247:1.16299
241015-23:35:48,340 nipype.interface INFO:
stdout 2024-10-15T23:35:48.340617:1.10025
241015-23:35:48,658 nipype.interface INFO:
stdout 2024-10-15T23:35:48.658024:1.5258
241015-23:35:48,988 nipype.interface INFO:
stdout 2024-10-15T23:35:48.988368:1.52019
241015-23:35:49,298 nipype.interface INFO:
stdout 2024-10-15T23:35:49.298043:0.0856617
241015-23:35:49,629 nipype.interface INFO:
stdout 2024-10-15T23:35:49.629311:0.125501
241015-23:35:49,904 nipype.interface INFO:
stdout 2024-10-15T23:35:49.904832:0.303064
241015-23:35:50,233 nipype.interface INFO:
stdout 2024-10-15T23:35:50.232979:0.10532
241015-23:35:50,521 nipype.interface INFO:
stdout 2024-10-15T23:35:50.521076:0.0578682
241015-23:35:50,721 nipype.workflow INFO:
[Node] Executing "fsl2itk" <niworkflows.interfaces.itk.MCFLIRT2ITK>
241015-23:35:50,722 nipype.interface WARNING:
Multithreading is deprecated. Remove the num_threads input.
241015-23:35:50,828 nipype.interface INFO:
stdout 2024-10-15T23:35:50.828505:0.0771756
241015-23:35:50,849 nipype.workflow INFO:
[Node] Finished "fsl2itk", elapsed time 0.12698s.
241015-23:35:51,166 nipype.interface INFO:
stdout 2024-10-15T23:35:51.166022:0.0968431
241015-23:35:51,451 nipype.interface INFO:
stdout 2024-10-15T23:35:51.451093:0.0749764
241015-23:35:51,748 nipype.interface INFO:
stdout 2024-10-15T23:35:51.748280:0.048651
241015-23:35:52,79 nipype.interface INFO:
stdout 2024-10-15T23:35:52.079501:0.0681753
241015-23:35:52,463 nipype.interface INFO:
stdout 2024-10-15T23:35:52.462974:0.0518362
241015-23:35:52,775 nipype.interface INFO:
stdout 2024-10-15T23:35:52.774957:0.0319023
241015-23:35:53,71 nipype.interface INFO:
stdout 2024-10-15T23:35:53.071594:0.276493
241015-23:35:53,245 nipype.workflow INFO:
[Node] Executing "fdisp" <nipype.algorithms.confounds.FramewiseDisplacement>
241015-23:35:53,248 nipype.workflow INFO:
[Node] Finished "fdisp", elapsed time 0.002118s.
241015-23:35:53,391 nipype.interface INFO:
stdout 2024-10-15T23:35:53.391627:0.141813
241015-23:35:53,725 nipype.interface INFO:
stdout 2024-10-15T23:35:53.725092:0.0882906
241015-23:35:54,46 nipype.interface INFO:
stdout 2024-10-15T23:35:54.046863:0.0525946
241015-23:35:54,369 nipype.interface INFO:
stdout 2024-10-15T23:35:54.369523:0.0251858
241015-23:35:54,687 nipype.interface INFO:
stdout 2024-10-15T23:35:54.687512:0.0809531
241015-23:35:54,998 nipype.interface INFO:
stdout 2024-10-15T23:35:54.998709:0.0723936
241015-23:35:55,287 nipype.interface INFO:
stdout 2024-10-15T23:35:55.287340:0.085268
241015-23:35:55,602 nipype.interface INFO:
stdout 2024-10-15T23:35:55.602434:0.0905847
241015-23:35:55,906 nipype.interface INFO:
stdout 2024-10-15T23:35:55.906214:0.0575284
241015-23:35:56,210 nipype.interface INFO:
stdout 2024-10-15T23:35:56.210119:0.0871247
241015-23:35:56,495 nipype.interface INFO:
stdout 2024-10-15T23:35:56.495360:0.209896
241015-23:35:56,770 nipype.interface INFO:
stdout 2024-10-15T23:35:56.770834:0.192506
241015-23:35:57,69 nipype.interface INFO:
stdout 2024-10-15T23:35:57.068991:0.0644833
241015-23:35:57,352 nipype.interface INFO:
stdout 2024-10-15T23:35:57.352098:0.0497486
241015-23:35:57,633 nipype.interface INFO:
stdout 2024-10-15T23:35:57.632991:0.0218686
241015-23:35:57,903 nipype.interface INFO:
stdout 2024-10-15T23:35:57.903487:0.0492257
241015-23:35:58,202 nipype.interface INFO:
stdout 2024-10-15T23:35:58.202372:0.0775428
241015-23:35:58,502 nipype.interface INFO:
stdout 2024-10-15T23:35:58.502322:0.298626
241015-23:35:58,787 nipype.interface INFO:
stdout 2024-10-15T23:35:58.787929:0.278837
241015-23:35:59,89 nipype.interface INFO:
stdout 2024-10-15T23:35:59.089817:0.0498628
241015-23:35:59,407 nipype.interface INFO:
stdout 2024-10-15T23:35:59.407364:0.0647269
241015-23:35:59,742 nipype.interface INFO:
stdout 2024-10-15T23:35:59.742648:0.0989051
241015-23:36:00,19 nipype.interface INFO:
stdout 2024-10-15T23:36:00.019510:0.0821868
241015-23:36:00,306 nipype.interface INFO:
stdout 2024-10-15T23:36:00.306269:0.0826831
241015-23:36:00,625 nipype.interface INFO:
stdout 2024-10-15T23:36:00.625903:0.089464
241015-23:36:00,937 nipype.interface INFO:
stdout 2024-10-15T23:36:00.936951:0.0412687
241015-23:36:01,328 nipype.interface INFO:
stdout 2024-10-15T23:36:01.328125:0.185584
241015-23:36:01,637 nipype.interface INFO:
stdout 2024-10-15T23:36:01.637702:0.170749
241015-23:36:01,935 nipype.interface INFO:
stdout 2024-10-15T23:36:01.935573:0.149975
241015-23:36:02,217 nipype.interface INFO:
stdout 2024-10-15T23:36:02.217500:0.0924617
241015-23:36:02,499 nipype.interface INFO:
stdout 2024-10-15T23:36:02.499232:0.216905
241015-23:36:02,785 nipype.interface INFO:
stdout 2024-10-15T23:36:02.785309:0.0928228
241015-23:36:03,64 nipype.interface INFO:
stdout 2024-10-15T23:36:03.064532:0.0413924
241015-23:36:03,393 nipype.interface INFO:
stdout 2024-10-15T23:36:03.393238:0.10436
241015-23:36:03,767 nipype.interface INFO:
stdout 2024-10-15T23:36:03.767474:0.0289767
241015-23:36:04,74 nipype.interface INFO:
stdout 2024-10-15T23:36:04.074882:0.0898213
241015-23:36:04,392 nipype.interface INFO:
stdout 2024-10-15T23:36:04.392788:0.0515129
241015-23:36:04,715 nipype.interface INFO:
stdout 2024-10-15T23:36:04.715741:0.175913
241015-23:36:04,989 nipype.interface INFO:
stdout 2024-10-15T23:36:04.989568:0.298548
241015-23:36:05,294 nipype.interface INFO:
stdout 2024-10-15T23:36:05.294689:0.462496
241015-23:36:05,573 nipype.interface INFO:
stdout 2024-10-15T23:36:05.573812:0.270213
241015-23:36:05,847 nipype.interface INFO:
stdout 2024-10-15T23:36:05.847937:0.0738641
241015-23:36:06,130 nipype.interface INFO:
stdout 2024-10-15T23:36:06.130243:0.0698636
241015-23:36:06,545 nipype.interface INFO:
stdout 2024-10-15T23:36:06.545827:0.168754
241015-23:36:06,849 nipype.interface INFO:
stdout 2024-10-15T23:36:06.848900:0.16513
241015-23:36:07,155 nipype.interface INFO:
stdout 2024-10-15T23:36:07.155903:0.0851289
241015-23:36:07,430 nipype.interface INFO:
stdout 2024-10-15T23:36:07.429990:0.0468945
241015-23:36:07,762 nipype.interface INFO:
stdout 2024-10-15T23:36:07.762281:0.166127
241015-23:36:08,62 nipype.interface INFO:
stdout 2024-10-15T23:36:08.062575:0.16282
241015-23:36:08,363 nipype.interface INFO:
stdout 2024-10-15T23:36:08.363400:0.0952082
241015-23:36:08,643 nipype.interface INFO:
stdout 2024-10-15T23:36:08.643217:0.356642
241015-23:36:08,974 nipype.interface INFO:
stdout 2024-10-15T23:36:08.974186:0.19418
241015-23:36:09,298 nipype.interface INFO:
stdout 2024-10-15T23:36:09.298055:0.126888
241015-23:36:09,600 nipype.interface INFO:
stdout 2024-10-15T23:36:09.600312:0.0771863
241015-23:36:09,915 nipype.interface INFO:
stdout 2024-10-15T23:36:09.915893:0.0950141
241015-23:36:10,236 nipype.interface INFO:
stdout 2024-10-15T23:36:10.236892:0.142077
241015-23:36:10,562 nipype.interface INFO:
stdout 2024-10-15T23:36:10.562273:0.099221
241015-23:36:10,873 nipype.interface INFO:
stdout 2024-10-15T23:36:10.873279:0.0350795
241015-23:36:11,220 nipype.interface INFO:
stdout 2024-10-15T23:36:11.220160:0.186767
241015-23:36:11,550 nipype.interface INFO:
stdout 2024-10-15T23:36:11.550418:0.159825
241015-23:36:11,842 nipype.interface INFO:
stdout 2024-10-15T23:36:11.842267:0.121566
241015-23:36:12,129 nipype.interface INFO:
stdout 2024-10-15T23:36:12.129789:0.189876
241015-23:36:12,477 nipype.interface INFO:
stdout 2024-10-15T23:36:12.477450:0.0706398
241015-23:36:12,816 nipype.interface INFO:
stdout 2024-10-15T23:36:12.816247:0.0882779
241015-23:36:13,162 nipype.interface INFO:
stdout 2024-10-15T23:36:13.162418:0.171304
241015-23:36:13,483 nipype.interface INFO:
stdout 2024-10-15T23:36:13.483484:0.173009
241015-23:36:13,826 nipype.interface INFO:
stdout 2024-10-15T23:36:13.826326:0.120357
241015-23:36:14,131 nipype.interface INFO:
stdout 2024-10-15T23:36:14.131823:0.0658371
241015-23:36:14,446 nipype.interface INFO:
stdout 2024-10-15T23:36:14.446423:0.121672
241015-23:36:14,776 nipype.interface INFO:
stdout 2024-10-15T23:36:14.776803:0.106815
241015-23:36:15,102 nipype.interface INFO:
stdout 2024-10-15T23:36:15.102667:0.0278532
241015-23:36:15,394 nipype.interface INFO:
stdout 2024-10-15T23:36:15.394535:0.0698339
241015-23:36:15,733 nipype.interface INFO:
stdout 2024-10-15T23:36:15.733735:0.0624019
241015-23:36:16,19 nipype.interface INFO:
stdout 2024-10-15T23:36:16.019210:0.0846316
241015-23:36:16,283 nipype.interface INFO:
stdout 2024-10-15T23:36:16.283245:0.0567651
241015-23:36:16,624 nipype.interface INFO:
stdout 2024-10-15T23:36:16.623998:0.0564219
241015-23:36:16,908 nipype.interface INFO:
stdout 2024-10-15T23:36:16.908848:0.210797
241015-23:36:17,217 nipype.interface INFO:
stdout 2024-10-15T23:36:17.217598:0.107237
241015-23:36:17,255 nipype.workflow INFO:
[Node] Finished "_inu_n40", elapsed time 33.8069s.
241015-23:36:17,542 nipype.interface INFO:
stdout 2024-10-15T23:36:17.542867:0.111563
241015-23:36:17,888 nipype.interface INFO:
stdout 2024-10-15T23:36:17.888854:0.260858
241015-23:36:18,200 nipype.interface INFO:
stdout 2024-10-15T23:36:18.200660:0.18313
241015-23:36:18,472 nipype.interface INFO:
stdout 2024-10-15T23:36:18.472826:0.158311
241015-23:36:18,741 nipype.interface INFO:
stdout 2024-10-15T23:36:18.741789:0.0605256
241015-23:36:18,934 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.lap_target" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/lap_target".
241015-23:36:18,939 nipype.workflow INFO:
[Node] Executing "lap_target" <nipype.interfaces.ants.utils.ImageMath>
241015-23:36:19,13 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.res_target" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/res_target".
241015-23:36:19,16 nipype.workflow INFO:
[Node] Executing "res_target" <niworkflows.interfaces.nibabel.RegridToZooms>
241015-23:36:19,27 nipype.workflow INFO:
[Node] Finished "rmsdiff", elapsed time 34.060469s.
241015-23:36:20,795 nipype.workflow INFO:
[Node] Finished "res_target", elapsed time 1.777984s.
241015-23:36:22,870 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.init_aff" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/init_aff".
241015-23:36:22,886 nipype.workflow INFO:
[Node] Executing "init_aff" <nipype.interfaces.ants.utils.AI>
241015-23:36:28,153 nipype.workflow INFO:
[Node] Finished "lap_target", elapsed time 8.864422s.
241015-23:36:28,874 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.mrg_target" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/mrg_target".
241015-23:36:28,882 nipype.workflow INFO:
[Node] Executing "mrg_target" <nipype.interfaces.utility.base.Merge>
241015-23:36:28,886 nipype.workflow INFO:
[Node] Finished "mrg_target", elapsed time 0.000775s.
241015-23:36:54,456 nipype.workflow INFO:
[Node] Finished "init_aff", elapsed time 31.117898s.
241015-23:36:55,3 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.norm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/norm".
241015-23:36:55,15 nipype.workflow INFO:
[Node] Executing "norm" <niworkflows.interfaces.fixes.FixHeaderRegistration>
241015-23:37:50,827 nipype.workflow INFO:
[Node] Finished "init_aff", elapsed time 150.337216s.
241015-23:37:53,32 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.norm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/norm".
241015-23:37:53,41 nipype.workflow INFO:
[Node] Executing "norm" <niworkflows.interfaces.fixes.FixHeaderRegistration>
241015-23:37:55,981 nipype.workflow INFO:
[Node] Finished "norm", elapsed time 2.555342s.
241015-23:37:56,883 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.map_brainmask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/map_brainmask".
241015-23:37:56,891 nipype.workflow INFO:
[Node] Executing "map_brainmask" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
241015-23:37:58,185 nipype.workflow INFO:
[Node] Finished "map_brainmask", elapsed time 0.739941s.
241015-23:38:00,900 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.n4_correct" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/n4_correct".
241015-23:38:00,905 nipype.workflow INFO:
[Node] Executing "n4_correct" <niworkflows.interfaces.fixes.FixN4BiasFieldCorrection>
241015-23:38:02,357 nipype.workflow INFO:
[Node] Finished "n4_correct", elapsed time 1.4509750000000001s.
241015-23:38:02,899 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.skullstrip_first_pass" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/skullstrip_first_pass".
241015-23:38:02,903 nipype.workflow INFO:
[Node] Executing "skullstrip_first_pass" <nipype.interfaces.fsl.preprocess.BET>
241015-23:38:04,886 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.ds_aslreg_wf.raw_sources" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/ds_aslreg_wf/raw_sources".
241015-23:38:04,891 nipype.workflow INFO:
[Node] Executing "raw_sources" <nipype.interfaces.utility.wrappers.Function>
241015-23:38:04,894 nipype.workflow INFO:
[Node] Finished "raw_sources", elapsed time 0.001078s.
241015-23:38:04,897 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_std_wf.gen_ref" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_std_wf/_in_tuple_MNI152NLin2009cAsym.resnative/gen_ref".
241015-23:38:04,908 nipype.workflow INFO:
[Node] Executing "gen_ref" <niworkflows.interfaces.nibabel.GenerateSamplingReference>
241015-23:38:04,936 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_native_wf.aslref_asl" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_native_wf/aslref_asl".
241015-23:38:04,942 nipype.workflow INFO:
[Node] Executing "aslref_asl" <fmriprep.interfaces.resampling.ResampleSeries>
241015-23:38:05,331 nipype.workflow INFO:
[Node] Finished "skullstrip_first_pass", elapsed time 2.425698s.
241015-23:38:06,915 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.first_dilate" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/first_dilate".
241015-23:38:06,921 nipype.workflow INFO:
[Node] Executing "first_dilate" <niworkflows.interfaces.nibabel.BinaryDilation>
241015-23:38:07,182 nipype.workflow INFO:
[Node] Finished "first_dilate", elapsed time 0.25848s.
241015-23:38:07,185 nipype.workflow INFO:
[Node] Finished "gen_ref", elapsed time 2.275337s.
241015-23:38:07,854 nipype.workflow INFO:
[Node] Finished "aslref_asl", elapsed time 2.911506s.
241015-23:38:08,913 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.first_mask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/first_mask".
241015-23:38:08,917 nipype.workflow INFO:
[Node] Executing "first_mask" <niworkflows.interfaces.nibabel.ApplyMask>
241015-23:38:08,942 nipype.workflow INFO:
[Node] Finished "first_mask", elapsed time 0.024383s.
241015-23:38:10,959 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.unifize" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/unifize".
241015-23:38:10,963 nipype.workflow INFO:
[Node] Executing "unifize" <nipype.interfaces.afni.utils.Unifize>
241015-23:38:52,390 nipype.workflow INFO:
[Node] Finished "unifize", elapsed time 41.424875s.
241015-23:38:52,984 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.fixhdr_unifize" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/fixhdr_unifize".
241015-23:38:53,83 nipype.workflow INFO:
[Node] Executing "fixhdr_unifize" <niworkflows.interfaces.header.CopyXForm>
241015-23:38:53,110 nipype.workflow INFO:
[Node] Finished "fixhdr_unifize", elapsed time 0.025915s.
241015-23:38:55,54 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.skullstrip_second_pass" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/skullstrip_second_pass".
241015-23:38:55,69 nipype.workflow INFO:
[Node] Executing "skullstrip_second_pass" <nipype.interfaces.afni.preprocess.Automask>
241015-23:38:55,448 nipype.workflow INFO:
[Node] Finished "skullstrip_second_pass", elapsed time 0.377396s.
241015-23:38:56,976 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.fixhdr_skullstrip2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/fixhdr_skullstrip2".
241015-23:38:57,49 nipype.workflow INFO:
[Node] Executing "fixhdr_skullstrip2" <niworkflows.interfaces.header.CopyXForm>
241015-23:38:57,72 nipype.workflow INFO:
[Node] Finished "fixhdr_skullstrip2", elapsed time 0.02123s.
241015-23:38:59,47 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.combine_masks" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/combine_masks".
241015-23:38:59,232 nipype.workflow INFO:
[Node] Executing "combine_masks" <nipype.interfaces.fsl.maths.BinaryMaths>
241015-23:38:59,408 nipype.workflow INFO:
[Node] Finished "combine_masks", elapsed time 0.174483s.
241015-23:39:00,990 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_fit_wf.enhance_aslref_wf.apply_mask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_fit_wf/enhance_aslref_wf/apply_mask".
241015-23:39:00,994 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.asl_preproc_asl.asl_confounds_wf.dvars" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/asl_preproc_asl/asl_confounds_wf/dvars".
241015-23:39:01,130 nipype.workflow INFO:
[Node] Executing "apply_mask" <niworkflows.interfaces.nibabel.ApplyMask>
241015-23:39:01,163 nipype.workflow INFO:
[Node] Executing "dvars" <nipype.algorithms.confounds.ComputeDVARS>
241015-23:39:01,174 nipype.workflow INFO:
[Node] Finished "apply_mask", elapsed time 0.042512s.
241015-23:39:05,322 nipype.workflow INFO:
[Node] Finished "dvars", elapsed time 4.157649s.
241015-23:46:46,733 nipype.workflow INFO:
[Node] Finished "norm", elapsed time 591.231926s.
241015-23:46:49,50 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.map_brainmask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/map_brainmask".
241015-23:46:49,51 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.map_wmmask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/map_wmmask".
241015-23:46:49,58 nipype.workflow INFO:
[Node] Executing "map_brainmask" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
241015-23:46:49,78 nipype.workflow INFO:
[Node] Executing "map_wmmask" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
241015-23:47:06,335 nipype.workflow INFO:
[Node] Finished "map_wmmask", elapsed time 16.739302s.
241015-23:47:07,243 nipype.workflow INFO:
[Node] Setting-up "_inu_n4_final0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0".
241015-23:47:07,246 nipype.workflow INFO:
[Node] Executing "_inu_n4_final0" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
241015-23:47:13,18 nipype.workflow INFO:
[Node] Finished "map_brainmask", elapsed time 23.959311s.
241015-23:47:15,232 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.thr_brainmask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/thr_brainmask".
241015-23:47:15,243 nipype.workflow INFO:
[Node] Executing "thr_brainmask" <nipype.interfaces.ants.utils.ThresholdImage>
241015-23:47:17,756 nipype.workflow INFO:
[Node] Finished "thr_brainmask", elapsed time 1.6254659999999999s.
241015-23:47:19,70 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.dil_brainmask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/dil_brainmask".
241015-23:47:19,72 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/03_pad_mask".
241015-23:47:19,79 nipype.workflow INFO:
[Node] Executing "03_pad_mask" <nipype.interfaces.ants.utils.ImageMath>
241015-23:47:19,82 nipype.workflow INFO:
[Node] Executing "dil_brainmask" <nipype.interfaces.ants.utils.ImageMath>
241015-23:47:21,89 nipype.workflow INFO:
[Node] Finished "03_pad_mask", elapsed time 1.289053s.
241015-23:47:21,231 nipype.workflow INFO:
[Node] Finished "dil_brainmask", elapsed time 2.145244s.
241015-23:47:23,57 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.get_brainmask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/get_brainmask".
241015-23:47:23,64 nipype.workflow INFO:
[Node] Executing "get_brainmask" <nipype.interfaces.ants.utils.ImageMath>
241015-23:47:25,695 nipype.workflow INFO:
[Node] Finished "get_brainmask", elapsed time 1.980961s.
241015-23:47:28,819 nipype.workflow INFO:
[Node] Finished "_inu_n4_final0", elapsed time 20.891908s.
241015-23:47:31,175 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/01_atropos".
241015-23:47:31,183 nipype.workflow INFO:
[Node] Setting-up "_apply_mask0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0".
241015-23:47:31,186 nipype.workflow INFO:
[Node] Executing "01_atropos" <nipype.interfaces.ants.segmentation.Atropos>
241015-23:47:31,187 nipype.workflow INFO:
[Node] Executing "_apply_mask0" <niworkflows.interfaces.nibabel.ApplyMask>
241015-23:47:32,258 nipype.workflow INFO:
[Node] Finished "_apply_mask0", elapsed time 1.068499s.
241015-23:47:33,649 nipype.workflow INFO:
[Node] Finished "autorecon1", elapsed time 710.70345s.
241015-23:47:35,319 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.fsnative2t1w_xfm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm".
241015-23:47:35,331 nipype.workflow INFO:
[Node] Executing "fsnative2t1w_xfm" <niworkflows.interfaces.freesurfer.PatchedRobustRegister>
241015-23:48:18,953 nipype.workflow INFO:
[Node] Finished "01_atropos", elapsed time 47.765305s.
241015-23:48:21,105 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/02_pad_segm".
241015-23:48:21,115 nipype.workflow INFO:
[Node] Executing "02_pad_segm" <nipype.interfaces.ants.utils.ImageMath>
241015-23:48:22,979 nipype.workflow INFO:
[Node] Finished "02_pad_segm", elapsed time 1.862714s.
241015-23:48:28,51 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/04_sel_labels".
241015-23:48:28,59 nipype.workflow INFO:
[Node] Executing "04_sel_labels" <nipype.interfaces.utility.wrappers.Function>
241015-23:48:28,545 nipype.workflow INFO:
[Node] Finished "04_sel_labels", elapsed time 0.484541s.
241015-23:48:30,1 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/10_me_csf".
241015-23:48:30,2 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/27_depad_csf".
241015-23:48:30,2 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/05_get_wm".
241015-23:48:30,3 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/06_get_gm".
241015-23:48:30,7 nipype.workflow INFO:
[Node] Executing "27_depad_csf" <nipype.interfaces.ants.utils.ImageMath>
241015-23:48:30,8 nipype.workflow INFO:
[Node] Executing "10_me_csf" <nipype.interfaces.ants.utils.ImageMath>
241015-23:48:30,10 nipype.workflow INFO:
[Node] Executing "05_get_wm" <nipype.interfaces.ants.utils.ImageMath>
241015-23:48:30,11 nipype.workflow INFO:
[Node] Executing "06_get_gm" <nipype.interfaces.ants.utils.ImageMath>
241015-23:48:31,309 nipype.workflow INFO:
[Node] Finished "27_depad_csf", elapsed time 1.300335s.
241015-23:48:32,26 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.apply_wm_prior" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/apply_wm_prior".
241015-23:48:32,33 nipype.workflow INFO:
[Node] Executing "apply_wm_prior" <nipype.interfaces.utility.wrappers.Function>
241015-23:48:32,403 nipype.workflow INFO:
[Node] Finished "05_get_wm", elapsed time 2.390829s.
241015-23:48:32,648 nipype.workflow INFO:
[Node] Finished "06_get_gm", elapsed time 2.635659s.
241015-23:48:33,151 nipype.workflow INFO:
[Node] Finished "apply_wm_prior", elapsed time 1.117009s.
241015-23:48:33,978 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/09_relabel_wm".
241015-23:48:33,979 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/07_fill_gm".
241015-23:48:33,983 nipype.workflow INFO:
[Node] Executing "09_relabel_wm" <nipype.interfaces.ants.utils.MultiplyImages>
241015-23:48:33,984 nipype.workflow INFO:
[Node] Executing "07_fill_gm" <nipype.interfaces.ants.utils.ImageMath>
241015-23:48:33,991 nipype.workflow INFO:
[Node] Setting-up "_inu_n4_final0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/inu_n4_final/mapflow/_inu_n4_final0".
241015-23:48:33,995 nipype.workflow INFO:
[Node] Executing "_inu_n4_final0" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
241015-23:48:35,374 nipype.workflow INFO:
[Node] Finished "09_relabel_wm", elapsed time 1.38923s.
241015-23:48:35,988 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/26_depad_wm".
241015-23:48:35,993 nipype.workflow INFO:
[Node] Executing "26_depad_wm" <nipype.interfaces.ants.utils.ImageMath>
241015-23:48:36,303 nipype.workflow INFO:
[Node] Finished "10_me_csf", elapsed time 6.293826s.
241015-23:48:37,679 nipype.workflow INFO:
[Node] Finished "26_depad_wm", elapsed time 1.6841080000000002s.
241015-23:48:38,898 nipype.workflow INFO:
[Node] Finished "fsnative2t1w_xfm", elapsed time 63.565442s.
241015-23:48:47,223 nipype.workflow INFO:
[Node] Finished "07_fill_gm", elapsed time 13.237835s.
241015-23:48:48,141 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/08_mult_gm".
241015-23:48:48,148 nipype.workflow INFO:
[Node] Executing "08_mult_gm" <nipype.interfaces.ants.utils.MultiplyImages>
241015-23:48:49,834 nipype.workflow INFO:
[Node] Finished "08_mult_gm", elapsed time 1.684894s.
241015-23:48:52,143 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/11_add_gm".
241015-23:48:52,150 nipype.workflow INFO:
[Node] Executing "11_add_gm" <nipype.interfaces.ants.utils.ImageMath>
241015-23:48:54,688 nipype.workflow INFO:
[Node] Finished "11_add_gm", elapsed time 2.536949s.
241015-23:48:56,146 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/12_relabel_gm".
241015-23:48:56,153 nipype.workflow INFO:
[Node] Executing "12_relabel_gm" <nipype.interfaces.ants.utils.MultiplyImages>
241015-23:48:56,530 nipype.workflow INFO:
[Node] Finished "_inu_n4_final0", elapsed time 22.533337s.
241015-23:48:57,657 nipype.workflow INFO:
[Node] Finished "12_relabel_gm", elapsed time 1.503458s.
241015-23:49:00,66 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm".
241015-23:49:00,66 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/25_depad_gm".
241015-23:49:00,71 nipype.workflow INFO:
[Node] Executing "13_add_gm_wm" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:00,71 nipype.workflow INFO:
[Node] Executing "25_depad_gm" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:01,785 nipype.workflow INFO:
[Node] Finished "25_depad_gm", elapsed time 1.711786s.
241015-23:49:02,721 nipype.workflow INFO:
[Node] Finished "13_add_gm_wm", elapsed time 2.648527s.
241015-23:49:04,192 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/14_sel_labels2".
241015-23:49:04,192 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/24_depad_segm".
241015-23:49:04,193 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/merge_tpms".
241015-23:49:04,198 nipype.workflow INFO:
[Node] Executing "24_depad_segm" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:04,198 nipype.workflow INFO:
[Node] Executing "14_sel_labels2" <nipype.interfaces.utility.wrappers.Function>
241015-23:49:04,200 nipype.workflow INFO:
[Node] Executing "merge_tpms" <nipype.interfaces.utility.base.Merge>
241015-23:49:04,201 nipype.workflow INFO:
[Node] Finished "merge_tpms", elapsed time 0.000437s.
241015-23:49:04,454 nipype.workflow INFO:
[Node] Finished "14_sel_labels2", elapsed time 0.254187s.
241015-23:49:05,732 nipype.workflow INFO:
[Node] Finished "24_depad_segm", elapsed time 1.533525s.
241015-23:49:06,55 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/15_add_7".
241015-23:49:06,58 nipype.workflow INFO:
[Node] Executing "15_add_7" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:08,266 nipype.workflow INFO:
[Node] Finished "15_add_7", elapsed time 2.206661s.
241015-23:49:10,110 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/16_me_7".
241015-23:49:10,115 nipype.workflow INFO:
[Node] Executing "16_me_7" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:14,5 nipype.workflow INFO:
[Node] Finished "16_me_7", elapsed time 3.888438s.
241015-23:49:16,116 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/17_comp_7".
241015-23:49:16,122 nipype.workflow INFO:
[Node] Executing "17_comp_7" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:18,799 nipype.workflow INFO:
[Node] Finished "17_comp_7", elapsed time 2.675638s.
241015-23:49:20,61 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/18_md_7".
241015-23:49:20,67 nipype.workflow INFO:
[Node] Executing "18_md_7" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:22,552 nipype.workflow INFO:
[Node] Finished "18_md_7", elapsed time 2.483126s.
241015-23:49:23,907 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/19_fill_7".
241015-23:49:23,912 nipype.workflow INFO:
[Node] Executing "19_fill_7" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:35,637 nipype.workflow INFO:
[Node] Finished "19_fill_7", elapsed time 11.723917s.
241015-23:49:36,21 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/20_add_7_2".
241015-23:49:36,28 nipype.workflow INFO:
[Node] Executing "20_add_7_2" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:38,471 nipype.workflow INFO:
[Node] Finished "20_add_7_2", elapsed time 1.861071s.
241015-23:49:40,73 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/21_md_7_2".
241015-23:49:40,79 nipype.workflow INFO:
[Node] Executing "21_md_7_2" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:42,739 nipype.workflow INFO:
[Node] Finished "21_md_7_2", elapsed time 2.6590160000000003s.
241015-23:49:44,73 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/22_me_7_2".
241015-23:49:44,78 nipype.workflow INFO:
[Node] Executing "22_me_7_2" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:48,261 nipype.workflow INFO:
[Node] Finished "22_me_7_2", elapsed time 4.181631s.
241015-23:49:49,947 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/23_depad_mask".
241015-23:49:49,954 nipype.workflow INFO:
[Node] Executing "23_depad_mask" <nipype.interfaces.ants.utils.ImageMath>
241015-23:49:51,187 nipype.workflow INFO:
[Node] Finished "23_depad_mask", elapsed time 1.231229s.
241015-23:49:52,19 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.msk_conform" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/msk_conform".
241015-23:49:52,26 nipype.workflow INFO:
[Node] Executing "msk_conform" <nipype.interfaces.utility.wrappers.Function>
241015-23:49:52,368 nipype.workflow INFO:
[Node] Finished "msk_conform", elapsed time 0.341015s.
241015-23:50:02,243 nipype.workflow INFO:
[Node] Setting-up "_apply_mask0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/apply_mask/mapflow/_apply_mask0".
241015-23:50:02,245 nipype.workflow INFO:
[Node] Executing "_apply_mask0" <niworkflows.interfaces.nibabel.ApplyMask>
241015-23:50:03,277 nipype.workflow INFO:
[Node] Finished "_apply_mask0", elapsed time 1.030496s.
241015-23:50:06,856 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.register_template_wf.trunc_mov" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/trunc_mov".
241015-23:50:06,857 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.ds_std_volumes_wf.gen_ref" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin2009cAsym.resnative/gen_ref".
241015-23:50:06,862 nipype.workflow INFO:
[Node] Executing "trunc_mov" <nipype.interfaces.ants.utils.ImageMath>
241015-23:50:08,509 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.skull_strip_extern" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/skull_strip_extern".
241015-23:50:09,295 nipype.workflow INFO:
[Node] Executing "gen_ref" <niworkflows.interfaces.nibabel.GenerateSamplingReference>
241015-23:50:11,156 nipype.workflow INFO:
[Node] Executing "skull_strip_extern" <niworkflows.interfaces.freesurfer.FSInjectBrainExtracted>
241015-23:50:13,427 nipype.workflow INFO:
[Node] Finished "trunc_mov", elapsed time 6.563622s.
241015-23:50:13,620 nipype.workflow INFO:
[Node] Finished "gen_ref", elapsed time 4.323494s.
241015-23:50:15,277 nipype.workflow INFO:
[Node] Finished "skull_strip_extern", elapsed time 4.119662s.
241015-23:50:20,870 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.gcareg" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/gcareg".
241015-23:50:20,874 nipype.workflow INFO:
[Node] Executing "gcareg" <smriprep.interfaces.freesurfer.ReconAll>
241015-23:50:20,876 nipype.interface INFO:
resume recon-all : recon-all -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -gcareg
241015-23:50:20,877 nipype.interface INFO:
resume recon-all : recon-all -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -gcareg
241015-23:54:44,373 nipype.workflow INFO:
[Node] Finished "gcareg", elapsed time 263.497329s.
241015-23:54:45,45 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
241015-23:54:45,54 nipype.workflow INFO:
[Node] Executing "autorecon2_vol" <smriprep.interfaces.freesurfer.ReconAll>
241015-23:54:45,57 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -nogcareg
241015-23:54:45,60 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -nogcareg
241016-01:55:38,518 nipype.workflow INFO:
[Node] Finished "autorecon2_vol", elapsed time 7253.461031s.
241016-01:55:41,204 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
241016-01:55:41,204 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
241016-01:55:41,216 nipype.workflow INFO:
[Node] Executing "_autorecon_surfs0" <smriprep.interfaces.freesurfer.ReconAll>
241016-01:55:41,218 nipype.workflow INFO:
[Node] Executing "_autorecon_surfs1" <smriprep.interfaces.freesurfer.ReconAll>
241016-01:55:41,223 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -rh-only -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer
241016-01:55:41,224 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -rh-only -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer
241016-01:55:41,222 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -lh-only -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer
241016-01:55:41,230 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -lh-only -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer
241016-02:33:50,646 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0", elapsed time 2289.426188s.
241016-02:35:29,761 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1", elapsed time 2388.538778s.
241016-02:35:31,748 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
241016-02:35:31,754 nipype.workflow INFO:
[Node] Executing "_autorecon_surfs0" <smriprep.interfaces.freesurfer.ReconAll>
241016-02:35:31,758 nipype.interface INFO:
recon-all complete : Not running
241016-02:35:31,759 nipype.interface INFO:
recon-all complete : Not running
241016-02:35:32,310 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0", elapsed time 0.553482s.
241016-02:35:32,318 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
241016-02:35:32,322 nipype.workflow INFO:
[Node] Executing "_autorecon_surfs1" <smriprep.interfaces.freesurfer.ReconAll>
241016-02:35:32,324 nipype.interface INFO:
recon-all complete : Not running
241016-02:35:32,325 nipype.interface INFO:
recon-all complete : Not running
241016-02:35:32,524 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1", elapsed time 0.201104s.
241016-02:35:35,654 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/cortribbon".
241016-02:35:35,660 nipype.workflow INFO:
[Node] Executing "cortribbon" <smriprep.interfaces.freesurfer.ReconAll>
241016-02:35:35,661 nipype.interface INFO:
resume recon-all : recon-all -parallel -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -cortribbon
241016-02:35:35,662 nipype.interface INFO:
resume recon-all : recon-all -parallel -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -cortribbon
241016-02:43:04,298 nipype.workflow INFO:
[Node] Finished "cortribbon", elapsed time 448.636713s.
241016-02:43:07,861 nipype.workflow INFO:
[Node] Setting-up "_parcstats0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
241016-02:43:07,863 nipype.workflow INFO:
[Node] Setting-up "_parcstats1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
241016-02:43:07,873 nipype.workflow INFO:
[Node] Executing "_parcstats0" <smriprep.interfaces.freesurfer.ReconAll>
241016-02:43:07,874 nipype.workflow INFO:
[Node] Executing "_parcstats1" <smriprep.interfaces.freesurfer.ReconAll>
241016-02:43:07,879 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -lh-only -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
241016-02:43:07,880 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -lh-only -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
241016-02:43:07,879 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -rh-only -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
241016-02:43:07,886 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -rh-only -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
241016-02:48:29,720 nipype.workflow INFO:
[Node] Finished "_parcstats0", elapsed time 321.84365s.
241016-02:48:31,471 nipype.workflow INFO:
[Node] Finished "_parcstats1", elapsed time 323.593271s.
241016-02:48:32,59 nipype.workflow INFO:
[Node] Setting-up "_parcstats0" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
241016-02:48:32,65 nipype.workflow INFO:
[Node] Executing "_parcstats0" <smriprep.interfaces.freesurfer.ReconAll>
241016-02:48:32,70 nipype.interface INFO:
recon-all complete : Not running
241016-02:48:32,71 nipype.interface INFO:
recon-all complete : Not running
241016-02:48:32,825 nipype.workflow INFO:
[Node] Finished "_parcstats0", elapsed time 0.756917s.
241016-02:48:32,834 nipype.workflow INFO:
[Node] Setting-up "_parcstats1" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
241016-02:48:32,838 nipype.workflow INFO:
[Node] Executing "_parcstats1" <smriprep.interfaces.freesurfer.ReconAll>
241016-02:48:32,840 nipype.interface INFO:
recon-all complete : Not running
241016-02:48:32,841 nipype.interface INFO:
recon-all complete : Not running
241016-02:48:33,183 nipype.workflow INFO:
[Node] Finished "_parcstats1", elapsed time 0.343395s.
241016-02:48:34,42 nipype.workflow INFO:
[Node] Setting-up "aslprep_0_7_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/home/jovyan/example-notebooks/books/functional_imaging/aslprep-work/aslprep_0_7_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/autorecon3".
241016-02:48:34,57 nipype.workflow INFO:
[Node] Executing "autorecon3" <smriprep.interfaces.freesurfer.ReconAll>
241016-02:48:34,62 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels
241016-02:48:34,63 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-01 -sd /home/jovyan/example-notebooks/books/functional_imaging/aslprep-output/sourcedata/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels
(node:14285) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
aslprep Results#
The full result report is in aslprep-output/sub-01.html and you can open this webpage in Jupyterlab or in the browser. Here a few items from the report as an example and for a quick checking:
Brain mask and brain tissue segmentation of the T1w#
This panel shows the template T1-weighted image (if several T1w images were found), with contours delineating the detected brain mask and brain tissue segmentations.
from IPython.core.display import SVG
SVG(filename='aslprep-output/sub-01/figures/sub-01_dseg.svg')
Spatial normalization of the anatomical T1w reference#
Results of nonlinear alignment of the T1w reference one or more template space(s)
from IPython.core.display import SVG
SVG(filename='aslprep-output/sub-01/figures/sub-01_space-MNI152NLin2009cAsym_T1w.svg')
Surface reconstruction#
Surfaces (white and pial) reconstructed with FreeSurfer (recon-all) overlaid on the participant’s T1w template.
from IPython.core.display import SVG
SVG(filename='aslprep-output/sub-01/figures/sub-01_desc-reconall_T1w.svg')
Alignment of functional and anatomical MRI data (volume based)#
mri_coreg (FreeSurfer) was used to generate transformations from EPI space to T1 Space - bbregister refinement rejected. Note that Nearest Neighbor interpolation is used in the reportlets in order to highlight potential spin-history and other artifacts, whereas final images are resampled using Lanczos interpolation.
from IPython.core.display import SVG
SVG(filename='aslprep-output/sub-01/figures/sub-01_desc-coreg_asl.svg')
ASL Summary#
Summary statistics are plotted, which may reveal trends or artifacts in the ASL data. DVARS and FD show the standardized DVARS and framewise-displacement measures for each time point. A carpet plot shows the time series for all voxels within the brain mask. Voxels are grouped into cortical (blue), and subcortical (orange) gray matter, cerebellum (green) and white matter and CSF (red), indicated by the color map on the left-hand side.
from IPython.core.display import SVG
SVG(filename='aslprep-output/sub-01/figures/sub-01_desc-carpetplot_asl.svg')
CBF#
The maps plot cerebral blood flow (CBF) for basic CBF. The unit is mL/100 g/min.
from IPython.core.display import SVG
SVG(filename='aslprep-output/sub-01/figures/sub-01_desc-cbf_cbf.svg')
