-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
208 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| --- | ||
| procyamlversion: 3.0.0-dev.0 | ||
|
|
||
| description: fmriprep - https://fmriprep.org/en/stable/ | ||
|
|
||
| jobtemplate: job_template_v3.txt | ||
|
|
||
| containers: | ||
| - name: fmriprep | ||
| path: fmriprep_24.1.1.sif | ||
| source: docker://nipreps/fmriprep:24.1.1 | ||
|
|
||
| requirements: | ||
| walltime: 2-0 | ||
| memory: 24000 | ||
|
|
||
| inputs: | ||
| xnat: | ||
|
|
||
| filters: | ||
| - type: match | ||
| inputs: scan_t1,assr_fs/scan_t1 | ||
|
|
||
| scans: | ||
|
|
||
| - name: scan_t1 | ||
| types: T1,T1_PGPP,T1W_3D_TFE_new_SENSE | ||
| keep_multis: first | ||
| skip_unusable: true | ||
| resources: | ||
| - {resource: NIFTI, fmatch: '*.nii.gz', fdest: t1.nii.gz} | ||
| - {resource: JSON, fmatch: '*.json', fdest: t1.json} | ||
|
|
||
| - name: scan_fmri | ||
| types: Funct_Run1,REST*,Rest* | ||
| resources: | ||
| - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmri.nii.gz} | ||
| - {resource: JSON, fmatch: '*.json', fdest: fmri.json} | ||
|
|
||
| assessors: | ||
|
|
||
| - name: assr_fs | ||
| proctypes: freesurfer741_v2 | ||
| resources: | ||
| - {resource: SUBJECT, ftype: DIR, fdest: SUBJECT} | ||
|
|
||
| attrs: | ||
| - {varname: subject, object: session, attr: subject_label} | ||
| - {varname: session, object: session, attr: label} | ||
|
|
||
| outputs: | ||
| - {path: HTML, type: DIR, resource: HTML} | ||
| - {path: fmriprepBIDS, type: DIR, resource: fmriprepBIDS} | ||
|
|
||
|
|
||
| pre: | ||
| type: singularity_exec | ||
| container: fmriprep | ||
| args: >- | ||
| bash -c ' | ||
| mkdir /INPUTS/freesurfer && | ||
| mv /INPUTS/SUBJECT/SUBJECT /INPUTS/freesurfer/sub-{subject} && | ||
| cd /INPUTS && | ||
| curl -o fmriprep-prep.tar.gz -L https://github.com/baxpr/fmriprep-prep/archive/refs/tags/v1.5.1.tar.gz && | ||
| tar -zxf fmriprep-prep.tar.gz && | ||
| export PATH=/INPUTS/fmriprep-prep-1.5.1/src:\$PATH && | ||
| fmriprep-prep.sh | ||
| --t1_niigz /INPUTS/t1.nii.gz | ||
| --bids_dir /INPUTS/fmriprepBIDS | ||
| --sub {subject} | ||
| --ses {session} | ||
| --fmri_niigzs /INPUTS/fmri.nii.gz | ||
| --task rest | ||
| ' | ||
| command: | ||
| type: singularity_run | ||
| container: fmriprep | ||
| args: >- | ||
| --notrack | ||
| --work-dir /tmp | ||
| --output-spaces MNI152NLin6Asym | ||
| --ignore fieldmaps slicetiming | ||
| --fs-license-file /opt/license.txt | ||
| --fs-subjects-dir /INPUTS/freesurfer | ||
| /INPUTS/fmriprepBIDS | ||
| /OUTPUTS/fmriprepBIDS | ||
| participant | ||
| extraopts: --bind /data/mcr/centos7/FS6/license.txt:/opt/license.txt | ||
|
|
||
|
|
||
| # Here we do some extra gymnastics to copy the full HTML output to HTML resource | ||
| # without knowing the dirnames (due to changed subject label). | ||
| post: | ||
| type: singularity_exec | ||
| container: fmriprep | ||
| args: >- | ||
| bash -c ' | ||
| mkdir /OUTPUTS/HTML && | ||
| cp /OUTPUTS/fmriprepBIDS/sub-*.html /OUTPUTS/HTML && | ||
| cp -R /OUTPUTS/fmriprepBIDS/sub-* /OUTPUTS/HTML && | ||
| rm -fr /OUTPUTS/HTML/sub-*/ses-* && | ||
| rm -fr /OUTPUTS/HTML/sub-*/log | ||
| ' |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| --- | ||
| procyamlversion: 3.0.0-dev.0 | ||
|
|
||
| description: fmriprep - https://fmriprep.org/en/stable/ | ||
|
|
||
| jobtemplate: job_template_v3.txt | ||
|
|
||
| containers: | ||
| - name: fmriprep | ||
| path: fmriprep_24.1.1.sif | ||
| source: docker://nipreps/fmriprep:24.1.1 | ||
|
|
||
| requirements: | ||
| walltime: 2-0 | ||
| memory: 24000 | ||
|
|
||
| inputs: | ||
| xnat: | ||
|
|
||
| filters: | ||
| - type: match | ||
| inputs: scan_t1,assr_fs/scan_t1 | ||
|
|
||
| scans: | ||
|
|
||
| - name: scan_t1 | ||
| types: T1W_3D_TFE,T1W_3D_TFE_new | ||
| keep_multis: 2 | ||
| skip_unusable: true | ||
| resources: | ||
| - {resource: NIFTI, fmatch: '*.nii.gz', fdest: t1.nii.gz} | ||
| - {resource: JSON, fmatch: '*.json', fdest: t1.json} | ||
|
|
||
| - name: scan_fmri | ||
| types: Funct_Run1,REST*,Rest* | ||
| resources: | ||
| - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmri.nii.gz} | ||
| - {resource: JSON, fmatch: '*.json', fdest: fmri.json} | ||
|
|
||
| assessors: | ||
|
|
||
| - name: assr_fs | ||
| proctypes: freesurfer741_v2 | ||
| resources: | ||
| - {resource: SUBJECT, ftype: DIR, fdest: SUBJECT} | ||
|
|
||
| attrs: | ||
| - {varname: subject, object: session, attr: subject_label} | ||
| - {varname: session, object: session, attr: label} | ||
|
|
||
| outputs: | ||
| - {path: HTML, type: DIR, resource: HTML} | ||
| - {path: fmriprepBIDS, type: DIR, resource: fmriprepBIDS} | ||
|
|
||
|
|
||
| pre: | ||
| type: singularity_exec | ||
| container: fmriprep | ||
| args: >- | ||
| bash -c ' | ||
| mkdir /INPUTS/freesurfer && | ||
| mv /INPUTS/SUBJECT/SUBJECT /INPUTS/freesurfer/sub-{subject} && | ||
| cd /INPUTS && | ||
| curl -o fmriprep-prep.tar.gz -L https://github.com/baxpr/fmriprep-prep/archive/refs/tags/v1.5.1.tar.gz && | ||
| tar -zxf fmriprep-prep.tar.gz && | ||
| export PATH=/INPUTS/fmriprep-prep-1.5.1/src:\$PATH && | ||
| fmriprep-prep.sh | ||
| --t1_niigz /INPUTS/t1.nii.gz | ||
| --bids_dir /INPUTS/fmriprepBIDS | ||
| --sub {subject} | ||
| --ses {session} | ||
| --fmri_niigzs /INPUTS/fmri.nii.gz | ||
| --task rest | ||
| ' | ||
| command: | ||
| type: singularity_run | ||
| container: fmriprep | ||
| args: >- | ||
| --notrack | ||
| --work-dir /tmp | ||
| --output-spaces MNI152NLin6Asym | ||
| --ignore fieldmaps slicetiming | ||
| --fs-license-file /opt/license.txt | ||
| --fs-subjects-dir /INPUTS/freesurfer | ||
| /INPUTS/fmriprepBIDS | ||
| /OUTPUTS/fmriprepBIDS | ||
| participant | ||
| extraopts: --bind /data/mcr/centos7/FS6/license.txt:/opt/license.txt | ||
|
|
||
|
|
||
| # Here we do some extra gymnastics to copy the full HTML output to HTML resource | ||
| # without knowing the dirnames (due to changed subject label). | ||
| post: | ||
| type: singularity_exec | ||
| container: fmriprep | ||
| args: >- | ||
| bash -c ' | ||
| mkdir /OUTPUTS/HTML && | ||
| cp /OUTPUTS/fmriprepBIDS/sub-*.html /OUTPUTS/HTML && | ||
| cp -R /OUTPUTS/fmriprepBIDS/sub-* /OUTPUTS/HTML && | ||
| rm -fr /OUTPUTS/HTML/sub-*/ses-* && | ||
| rm -fr /OUTPUTS/HTML/sub-*/log | ||
| ' |