From d18208a3b9c9345c590f56152b8e261a2917f127 Mon Sep 17 00:00:00 2001 From: duettwe <61516027+duettwe@users.noreply.github.com> Date: Fri, 25 Jul 2025 13:45:37 -0500 Subject: [PATCH 1/5] Create fmriprep-GRUHN_v24.1.1.yaml --- processors/fmriprep-GRUHN_v24.1.1.yaml | 91 ++++++++++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 processors/fmriprep-GRUHN_v24.1.1.yaml diff --git a/processors/fmriprep-GRUHN_v24.1.1.yaml b/processors/fmriprep-GRUHN_v24.1.1.yaml new file mode 100644 index 0000000..bcd4fd3 --- /dev/null +++ b/processors/fmriprep-GRUHN_v24.1.1.yaml @@ -0,0 +1,91 @@ +--- +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 + resources: + - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmri.nii.gz} + - {resource: JSON, fmatch: '*.json', fdest: fmri.json} + - name: scan_fmrirpe + types: ERT_2 + 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 v1.5.0.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} + ' + From a78745fba6ffc4c572d5186fae8a90fb77329694 Mon Sep 17 00:00:00 2001 From: duettwe <61516027+duettwe@users.noreply.github.com> Date: Fri, 25 Jul 2025 14:23:17 -0500 Subject: [PATCH 2/5] Update fmriprep-GRUHN_v24.1.1.yaml --- processors/fmriprep-GRUHN_v24.1.1.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/processors/fmriprep-GRUHN_v24.1.1.yaml b/processors/fmriprep-GRUHN_v24.1.1.yaml index bcd4fd3..7fe31c5 100644 --- a/processors/fmriprep-GRUHN_v24.1.1.yaml +++ b/processors/fmriprep-GRUHN_v24.1.1.yaml @@ -52,9 +52,9 @@ pre: 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 && + 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 From 1b623f3f546cbe36bdd5214e9c3b8a784415fcc4 Mon Sep 17 00:00:00 2001 From: duettwe <61516027+duettwe@users.noreply.github.com> Date: Mon, 28 Jul 2025 08:48:57 -0500 Subject: [PATCH 3/5] Update fmriprep-GRUHN_v24.1.1.yaml --- processors/fmriprep-GRUHN_v24.1.1.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/processors/fmriprep-GRUHN_v24.1.1.yaml b/processors/fmriprep-GRUHN_v24.1.1.yaml index 7fe31c5..03edf70 100644 --- a/processors/fmriprep-GRUHN_v24.1.1.yaml +++ b/processors/fmriprep-GRUHN_v24.1.1.yaml @@ -23,12 +23,12 @@ inputs: - {resource: NIFTI, fmatch: '*.nii.gz', fdest: t1.nii.gz} - {resource: JSON, fmatch: '*.json', fdest: t1.json} - name: scan_fmri - types: ERT_1 + 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: ERT_2 + types: TopUp_GE_APP keep_multis: first resources: - {resource: NIFTI, fmatch: '*.nii.gz', fdest: fmrirpe.nii.gz} From 84c0c79d5e4ce3b973466932c5231f9aee677a5c Mon Sep 17 00:00:00 2001 From: duettwe <61516027+duettwe@users.noreply.github.com> Date: Tue, 29 Jul 2025 07:46:03 -0500 Subject: [PATCH 4/5] Update fmriprep-GRUHN_v24.1.1.yaml --- processors/fmriprep-GRUHN_v24.1.1.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/processors/fmriprep-GRUHN_v24.1.1.yaml b/processors/fmriprep-GRUHN_v24.1.1.yaml index 03edf70..fa094e6 100644 --- a/processors/fmriprep-GRUHN_v24.1.1.yaml +++ b/processors/fmriprep-GRUHN_v24.1.1.yaml @@ -69,7 +69,6 @@ command: container: fmriprep args: >- --notrack - --participant_label {subject} --output-spaces MNI152NLin6Asym --slice-time-ref 0 --fs-license-file /opt/license.txt @@ -84,8 +83,8 @@ post: 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} + cp /OUTPUTS/BIDS/sub-*.html /OUTPUTS/HTML && + mkdir /OUTPUTS/HTML/sub-* && + cp -R /OUTPUTS/BIDS/sub-*/figures /OUTPUTS/HTML/sub-* ' From 7e1c069e30ea763fc616a26e100b8b35ff824c32 Mon Sep 17 00:00:00 2001 From: duettwe <61516027+duettwe@users.noreply.github.com> Date: Mon, 4 Aug 2025 15:44:11 -0500 Subject: [PATCH 5/5] Update fmriprep-GRUHN_v24.1.1.yaml --- processors/fmriprep-GRUHN_v24.1.1.yaml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/processors/fmriprep-GRUHN_v24.1.1.yaml b/processors/fmriprep-GRUHN_v24.1.1.yaml index fa094e6..052e664 100644 --- a/processors/fmriprep-GRUHN_v24.1.1.yaml +++ b/processors/fmriprep-GRUHN_v24.1.1.yaml @@ -77,6 +77,8 @@ command: /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 @@ -84,7 +86,8 @@ post: bash -c ' mkdir /OUTPUTS/HTML && cp /OUTPUTS/BIDS/sub-*.html /OUTPUTS/HTML && - mkdir /OUTPUTS/HTML/sub-* && - cp -R /OUTPUTS/BIDS/sub-*/figures /OUTPUTS/HTML/sub-* + cp -R /OUTPUTS/BIDS/sub-* /OUTPUTS/HTML && + rm -fr /OUTPUTS/HTML/sub-*/ses-* && + rm -fr /OUTPUTS/HTML/sub-*/log '