From d6f4d0a4290ecfe175c63704a05d77ae9769c36e Mon Sep 17 00:00:00 2001 From: Baxter Rogers Date: Thu, 21 Nov 2024 10:34:27 -0600 Subject: [PATCH] proc --- processors/fmriprep-GF-st-topup_v24.1.1.yaml | 107 +++++++++++++++++++ processors/fmriprep-NVS-rest_v23.2.1.yaml | 107 +++++++++++++++++++ 2 files changed, 214 insertions(+) create mode 100644 processors/fmriprep-GF-st-topup_v24.1.1.yaml create mode 100644 processors/fmriprep-NVS-rest_v23.2.1.yaml diff --git a/processors/fmriprep-GF-st-topup_v24.1.1.yaml b/processors/fmriprep-GF-st-topup_v24.1.1.yaml new file mode 100644 index 0000000..d44649e --- /dev/null +++ b/processors/fmriprep-GF-st-topup_v24.1.1.yaml @@ -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_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: '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: rest1APA_FMRI_MB3_2_5mm_1300 + resources: + - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmri.nii.gz} + - {resource: JSON, fmatch: '*.json', fdest: fmri.json} + + - 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} + + 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 v1.5.0.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 + +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} + ' diff --git a/processors/fmriprep-NVS-rest_v23.2.1.yaml b/processors/fmriprep-NVS-rest_v23.2.1.yaml new file mode 100644 index 0000000..1e0d71b --- /dev/null +++ b/processors/fmriprep-NVS-rest_v23.2.1.yaml @@ -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} + + - 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} + '