diff --git a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml index 2b33ec9..779e68e 100644 --- a/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml +++ b/processors/fmriprep-DARBY-philips-def-k_v24.1.1.yaml @@ -1,6 +1,5 @@ # THIS IS STILL BEING TESTED!!!!!!!!!!!!!!!!!! # DON'T USE THIS YET!!!!!!!!!!!!!!!!!!!!!!!!!! - --- procyamlversion: 3.0.0-dev.0 @@ -46,7 +45,6 @@ inputs: - {varname: session, object: session, attr: label} outputs: - - {path: sourcedata, type: DIR, resource: sourcedata} - {path: HTML, type: DIR, resource: HTML} - {path: BIDS, type: DIR, resource: fmriprepBIDS} @@ -72,15 +70,18 @@ command: type: singularity_run container: fmriprep args: >- + --work-dir /tmp --notrack --output-spaces MNI152NLin2009cAsym - --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 +# 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 @@ -88,7 +89,7 @@ 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-* && - mv /OUTPUTS/BIDS/sourcedata /OUTPUTS/sourcedata + cp -R /OUTPUTS/BIDS/sub-* /OUTPUTS/HTML && + rm -fr /OUTPUTS/HTML/sub-*/ses-* && + rm -fr /OUTPUTS/HTML/sub-*/log '