diff --git a/processors/fmriprep-GRUHN_v24.1.1.yaml b/processors/fmriprep-GRUHN_v24.1.1.yaml new file mode 100644 index 0000000..052e664 --- /dev/null +++ b/processors/fmriprep-GRUHN_v24.1.1.yaml @@ -0,0 +1,93 @@ +--- +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: "48:00:00" + 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: ERT_1,ERT_2 + resources: + - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmri.nii.gz} + - {resource: JSON, fmatch: '*.json', fdest: fmri.json} + - name: scan_fmrirpe + types: TopUp_GE_APP + 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: freesurfer800_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 v1.6.1.tar.gz -L https://github.com/baxpr/fmriprep-prep/archive/refs/tags/v1.6.1.tar.gz && + tar -zxf v1.6.1.tar.gz && + export PATH=/INPUTS/fmriprep-prep-1.6.1/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 + --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 +# 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/BIDS/sub-*.html /OUTPUTS/HTML && + cp -R /OUTPUTS/BIDS/sub-* /OUTPUTS/HTML && + rm -fr /OUTPUTS/HTML/sub-*/ses-* && + rm -fr /OUTPUTS/HTML/sub-*/log + ' +