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ENH: Make bids the default output layout option #2555

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Sep 21, 2021
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ENH: Make bids the default output layout option #2555

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6855d05
ENH: Make bids the default output layout option
effigies Sep 21, 2021
f70000f
CI: Pass --output-layout legacy to CI runs
effigies Sep 21, 2021
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17 changes: 12 additions & 5 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -421,6 +421,7 @@ jobs:
--network none \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--output-layout legacy \
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
--skull-strip-template OASIS30ANTs:res-1 \
--output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \
Expand Down Expand Up @@ -453,6 +454,7 @@ jobs:
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
${FASTRACK_ARG} \
--output-layout legacy \
--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
--use-aroma \
--skull-strip-template OASIS30ANTs:res-1 \
Expand All @@ -472,9 +474,9 @@ jobs:
name: Checking outputs of full fMRIPrep run
command: |
mkdir -p /tmp/${DATASET}/test
CHECK_OUTPUTS_FILE="${DATASET}_fasttrack_outputs.txt"
CHECK_OUTPUTS_FILE="${DATASET}_legacy_fasttrack_outputs.txt"
if [ -f /tmp/.nofasttrack ]; then
CHECK_OUTPUTS_FILE="${DATASET}_outputs.txt"
CHECK_OUTPUTS_FILE="${DATASET}_legacy_outputs.txt"
fi
find /tmp/${DATASET}/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives/++ | sort > /tmp/${DATASET}/test/outputs.out
diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out
Expand All @@ -498,7 +500,6 @@ jobs:
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work_bids \
/tmp/data/${DATASET}/ /tmp/${DATASET}/bids participant \
${FASTRACK_ARG} \
--output-layout bids \
--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
--output-spaces MNI152NLin2009cAsym \
--nthreads 2 -vv
Expand Down Expand Up @@ -529,6 +530,7 @@ jobs:
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives_partial participant \
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
${FASTRACK_ARG} \
--output-layout legacy \
--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
--output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
--aroma-melodic-dimensionality 2 --use-aroma \
Expand All @@ -537,9 +539,9 @@ jobs:
name: Checking outputs of partial fMRIPrep run
command: |
mkdir -p /tmp/${DATASET}/test
CHECK_OUTPUTS_FILE="${DATASET}_partial_fasttrack_outputs.txt"
CHECK_OUTPUTS_FILE="${DATASET}_legacy_partial_fasttrack_outputs.txt"
if [ -f /tmp/.nofasttrack ]; then
CHECK_OUTPUTS_FILE="${DATASET}_partial_outputs.txt"
CHECK_OUTPUTS_FILE="${DATASET}_legacy_partial_outputs.txt"
fi
sudo rm -rf /tmp/${DATASET}/derivatives_partial/freesurfer
find /tmp/${DATASET}/derivatives_partial \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives_partial/++ | sort > /tmp/${DATASET}/test/outputs.out
Expand Down Expand Up @@ -649,6 +651,7 @@ jobs:
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--output-layout legacy \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem_mb 4096 --nthreads 2 --anat-only -vv
Expand Down Expand Up @@ -677,6 +680,7 @@ jobs:
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
${FASTRACK_ARG} \
--output-layout legacy \
--fs-no-reconall --sloppy \
--output-spaces MNI152NLin2009cAsym:res-2 anat func \
--mem_mb 4096 --nthreads 2 -vv --debug compcor
Expand Down Expand Up @@ -705,6 +709,7 @@ jobs:
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--output-layout legacy \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym:res-2 anat func \
--reports-only --config-file /tmp/${DATASET}/work/${UUID}/config.toml -vv
Expand Down Expand Up @@ -811,6 +816,7 @@ jobs:
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--output-layout legacy \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem_mb 4096 --nthreads 2 --anat-only -vv
Expand Down Expand Up @@ -839,6 +845,7 @@ jobs:
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
${FASTRACK_ARG} \
--output-layout legacy \
--fs-no-reconall --use-syn-sdc --ignore slicetiming \
--dummy-scans 1 --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
Expand Down
0 .circleci/ds005_fasttrack_outputs.txt → .circleci/ds005_legacy_fasttrack_outputs.txt
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0 .circleci/ds005_outputs.txt → .circleci/ds005_legacy_outputs.txt
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0 ...cleci/ds005_partial_fasttrack_outputs.txt → ...s005_legacy_partial_fasttrack_outputs.txt
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0 .circleci/ds005_partial_outputs.txt → .circleci/ds005_legacy_partial_outputs.txt
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8 changes: 4 additions & 4 deletions fmriprep/cli/parser.py
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Expand Up @@ -527,12 +527,12 @@ def _slice_time_ref(value, parser):
g_other.add_argument(
"--output-layout",
action="store",
default="legacy",
default="bids",
choices=("bids", "legacy"),
help="Organization of outputs. legacy (default) creates derivative "
"datasets as subdirectories of outputs. bids places fMRIPrep derivatives "
help="Organization of outputs. bids (default) places fMRIPrep derivatives "
"directly in the output directory, and defaults to placing FreeSurfer "
"derivatives in <output-dir>/sourcedata/freesurfer."
"derivatives in <output-dir>/sourcedata/freesurfer. legacy creates "
"derivative datasets as subdirectories of outputs."
)
g_other.add_argument(
"-w",
Expand Down