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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,107 @@ | ||
| --- | ||
| procyamlversion: 3.0.0-dev.0 | ||
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| description: fmriprep - https://fmriprep.org/en/stable/ | ||
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| jobtemplate: job_template_v3.txt | ||
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| containers: | ||
| - name: fmriprep | ||
| path: fmriprep_24.1.1.sif | ||
| source: docker://nipreps/fmriprep:24.1.1 | ||
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| requirements: | ||
| walltime: 2-0 | ||
| memory: 24000 | ||
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| inputs: | ||
| xnat: | ||
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| filters: | ||
| - type: match | ||
| inputs: scan_t1,assr_fs/scan_t1 | ||
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| scans: | ||
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| - name: scan_t1 | ||
| types: 'cs_T1W_3D_TFE_32 channel' | ||
| keep_multis: first | ||
| skip_unusable: true | ||
| resources: | ||
| - {resource: NIFTI, fmatch: '*.nii.gz', fdest: t1.nii.gz} | ||
| - {resource: JSON, fmatch: '*.json', fdest: t1.json} | ||
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| - name: scan_fmri | ||
| types: rest1APA_FMRI_MB3_2_5mm_1300 | ||
| resources: | ||
| - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmri.nii.gz} | ||
| - {resource: JSON, fmatch: '*.json', fdest: fmri.json} | ||
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| - name: scan_fmrirpe | ||
| types: rest2APP_FMRI_MB3_2_5mm_1300 | ||
| keep_multis: first | ||
| resources: | ||
| - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmrirpe.nii.gz} | ||
| - {resource: JSON, fmatch: '*.json', fdest: fmrirpe.json} | ||
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| assessors: | ||
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| - name: assr_fs | ||
| proctypes: freesurfer741_v2 | ||
| resources: | ||
| - {resource: SUBJECT, ftype: DIR, fdest: SUBJECT} | ||
|
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| attrs: | ||
| - {varname: subject, object: session, attr: subject_label} | ||
| - {varname: session, object: session, attr: label} | ||
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| outputs: | ||
| - {path: HTML, type: DIR, resource: HTML} | ||
| - {path: BIDS, type: DIR, resource: fmriprepBIDS} | ||
|
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| pre: | ||
| type: singularity_exec | ||
| container: fmriprep | ||
| args: >- | ||
| bash -c ' | ||
| mkdir /INPUTS/freesurfer && | ||
| mv /INPUTS/SUBJECT/SUBJECT /INPUTS/freesurfer/sub-{subject} && | ||
| cd /INPUTS && | ||
| curl -o v1.5.0.tar.gz -L https://github.com/baxpr/fmriprep-prep/archive/refs/tags/v1.5.0.tar.gz && | ||
| tar -zxf v1.5.0.tar.gz && | ||
| export PATH=/INPUTS/fmriprep-prep-1.5.0/src:\$PATH && | ||
| fmriprep-prep.sh | ||
| --t1_niigz /INPUTS/t1.nii.gz | ||
| --rpefwd_niigz /INPUTS/fmri.nii.gz | ||
| --rperev_niigz /INPUTS/fmrirpe.nii.gz | ||
| --bids_dir /INPUTS/BIDS | ||
| --sub {subject} | ||
| --ses {session} | ||
| --fmri_niigzs /INPUTS/fmri.nii.gz | ||
| ' | ||
| command: | ||
| type: singularity_run | ||
| container: fmriprep | ||
| args: >- | ||
| --notrack | ||
| --participant_label {subject} | ||
| --output-spaces MNI152NLin6Asym | ||
| --slice-time-ref 0 | ||
| --fs-license-file /opt/license.txt | ||
| --fs-subjects-dir /INPUTS/freesurfer | ||
| /INPUTS/BIDS | ||
| /OUTPUTS/BIDS | ||
| participant | ||
| extraopts: --bind /data/mcr/centos7/FS6/license.txt:/opt/license.txt | ||
|
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||
| post: | ||
| type: singularity_exec | ||
| container: fmriprep | ||
| args: >- | ||
| bash -c ' | ||
| mkdir /OUTPUTS/HTML && | ||
| cp /OUTPUTS/BIDS/sub-{subject}.html /OUTPUTS/HTML && | ||
| mkdir /OUTPUTS/HTML/sub-{subject} && | ||
| cp -R /OUTPUTS/BIDS/sub-{subject}/figures /OUTPUTS/HTML/sub-{subject} | ||
| ' |
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 +1,107 @@ | ||
| --- | ||
| procyamlversion: 3.0.0-dev.0 | ||
|
|
||
| description: fmriprep - https://fmriprep.org/en/stable/ | ||
|
|
||
| jobtemplate: job_template_v3.txt | ||
|
|
||
| containers: | ||
| - name: fmriprep | ||
| path: fmriprep_23.2.1.sif | ||
| source: docker://nipreps/fmriprep:23.2.1 | ||
|
|
||
| requirements: | ||
| walltime: 2-0 | ||
| memory: 24000 | ||
|
|
||
| inputs: | ||
| xnat: | ||
|
|
||
| filters: | ||
| - type: match | ||
| inputs: scan_t1,assr_fs/scan_t1 | ||
|
|
||
| scans: | ||
|
|
||
| - name: scan_t1 | ||
| types: 'cs_T1W_3D_TFE_32 channel' | ||
| 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: Rest | ||
| resources: | ||
| - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmri.nii.gz} | ||
| - {resource: JSON, fmatch: '*.json', fdest: fmri.json} | ||
|
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| - name: scan_fmrirpe | ||
| types: TOPUP | ||
| keep_multis: first | ||
| resources: | ||
| - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmrirpe.nii.gz} | ||
| - {resource: JSON, fmatch: '*.json', fdest: fmrirpe.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: BIDS, 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 v1.4.0.tar.gz -L https://github.com/baxpr/fmriprep-prep/archive/refs/tags/v1.4.0.tar.gz && | ||
| tar -zxf v1.4.0.tar.gz && | ||
| export PATH=/INPUTS/fmriprep-prep-1.4.0/src:\$PATH && | ||
| fmriprep-prep.sh | ||
| --t1_niigz /INPUTS/t1.nii.gz | ||
| --rpefwd_niigz /INPUTS/fmri.nii.gz | ||
| --rperev_niigz /INPUTS/fmrirpe.nii.gz | ||
| --bids_dir /INPUTS/BIDS | ||
| --sub {subject} | ||
| --ses {session} | ||
| --fmri_niigzs /INPUTS/fmri.nii.gz | ||
| ' | ||
| command: | ||
| type: singularity_run | ||
| container: fmriprep | ||
| args: >- | ||
| --notrack | ||
| --participant_label {subject} | ||
| --output-spaces MNI152NLin6Asym | ||
| --ignore slicetiming | ||
| --fs-license-file /opt/license.txt | ||
| --fs-subjects-dir /INPUTS/freesurfer | ||
| /INPUTS/BIDS | ||
| /OUTPUTS/BIDS | ||
| participant | ||
| extraopts: --bind /data/mcr/centos7/FS6/license.txt:/opt/license.txt | ||
|
|
||
| post: | ||
| type: singularity_exec | ||
| container: fmriprep | ||
| args: >- | ||
| bash -c ' | ||
| mkdir /OUTPUTS/HTML && | ||
| cp /OUTPUTS/BIDS/sub-{subject}.html /OUTPUTS/HTML && | ||
| mkdir /OUTPUTS/HTML/sub-{subject} && | ||
| cp -R /OUTPUTS/BIDS/sub-{subject}/figures /OUTPUTS/HTML/sub-{subject} | ||
| ' |