From 6855d05a6ec8098ce8bea12fbc34a57bddcb9f4e Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 21 Sep 2021 14:07:34 -0400 Subject: [PATCH 1/2] ENH: Make bids the default output layout option --- fmriprep/cli/parser.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py index da3c32cfb..ee88aff26 100644 --- a/fmriprep/cli/parser.py +++ b/fmriprep/cli/parser.py @@ -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 /sourcedata/freesurfer." + "derivatives in /sourcedata/freesurfer. legacy creates " + "derivative datasets as subdirectories of outputs." ) g_other.add_argument( "-w", From f70000f6efebec0f7a5a0219daeb15f78a7cba94 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 21 Sep 2021 14:43:59 -0400 Subject: [PATCH 2/2] CI: Pass --output-layout legacy to CI runs --- .circleci/config.yml | 17 ++++++++++++----- ...s.txt => ds005_legacy_fasttrack_outputs.txt} | 0 ...005_outputs.txt => ds005_legacy_outputs.txt} | 0 ... ds005_legacy_partial_fasttrack_outputs.txt} | 0 ...uts.txt => ds005_legacy_partial_outputs.txt} | 0 5 files changed, 12 insertions(+), 5 deletions(-) rename .circleci/{ds005_fasttrack_outputs.txt => ds005_legacy_fasttrack_outputs.txt} (100%) rename .circleci/{ds005_outputs.txt => ds005_legacy_outputs.txt} (100%) rename .circleci/{ds005_partial_fasttrack_outputs.txt => ds005_legacy_partial_fasttrack_outputs.txt} (100%) rename .circleci/{ds005_partial_outputs.txt => ds005_legacy_partial_outputs.txt} (100%) diff --git a/.circleci/config.yml b/.circleci/config.yml index 4aae607f1..327971190 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -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/${DATASET}/freesurfer \ --skull-strip-template OASIS30ANTs:res-1 \ --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \ @@ -453,6 +454,7 @@ jobs: /tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \ --fs-subjects-dir /tmp/${DATASET}/freesurfer \ ${FASTRACK_ARG} \ + --output-layout legacy \ --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \ --use-aroma \ --skull-strip-template OASIS30ANTs:res-1 \ @@ -472,9 +474,9 @@ jobs: name: Checking outputs of full fMRIPrep run command: | mkdir -p /tmp/${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 @@ -498,7 +500,6 @@ jobs: --config $PWD/nipype.cfg -w /tmp/${DATASET}/work_bids \ /tmp/data/${DATASET}/ /tmp/${DATASET}/bids participant \ ${FASTRACK_ARG} \ - --output-layout bids \ --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \ --output-spaces MNI152NLin2009cAsym \ --nthreads 2 -vv @@ -529,6 +530,7 @@ jobs: /tmp/data/${DATASET} /tmp/${DATASET}/derivatives_partial participant \ --fs-subjects-dir /tmp/${DATASET}/freesurfer \ ${FASTRACK_ARG} \ + --output-layout legacy \ --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \ --output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \ --aroma-melodic-dimensionality 2 --use-aroma \ @@ -537,9 +539,9 @@ jobs: name: Checking outputs of partial fMRIPrep run command: | mkdir -p /tmp/${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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 \ diff --git a/.circleci/ds005_fasttrack_outputs.txt b/.circleci/ds005_legacy_fasttrack_outputs.txt similarity index 100% rename from .circleci/ds005_fasttrack_outputs.txt rename to .circleci/ds005_legacy_fasttrack_outputs.txt diff --git a/.circleci/ds005_outputs.txt b/.circleci/ds005_legacy_outputs.txt similarity index 100% rename from .circleci/ds005_outputs.txt rename to .circleci/ds005_legacy_outputs.txt diff --git a/.circleci/ds005_partial_fasttrack_outputs.txt b/.circleci/ds005_legacy_partial_fasttrack_outputs.txt similarity index 100% rename from .circleci/ds005_partial_fasttrack_outputs.txt rename to .circleci/ds005_legacy_partial_fasttrack_outputs.txt diff --git a/.circleci/ds005_partial_outputs.txt b/.circleci/ds005_legacy_partial_outputs.txt similarity index 100% rename from .circleci/ds005_partial_outputs.txt rename to .circleci/ds005_legacy_partial_outputs.txt