From fb76080eacd0dd23fd12634a32d5c73b76ee5bf8 Mon Sep 17 00:00:00 2001 From: Soichi Hayashi Date: Wed, 26 Feb 2020 21:39:39 +0000 Subject: [PATCH 1/7] added various temp output to .gitignore --- .gitignore | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/.gitignore b/.gitignore index 61ecee9..6baffbb 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,18 @@ config.json testdata +anat/ +anat_mask/ +fmap.json +fmri.json +fmripinput/ +fmripout/ +license.txt +multi_proc.yml +product.json +regress/ +surface/ +t1w.json +t2w.json +templateflow/ +test.sh + From e673753581ab68d393e07dd6040d2003a526ad3b Mon Sep 17 00:00:00 2001 From: Soichi Hayashi Date: Wed, 26 Feb 2020 21:41:41 +0000 Subject: [PATCH 2/7] renaming output_report/fmriprep output_report/html --- main | 1 + 1 file changed, 1 insertion(+) diff --git a/main b/main index 1e18fb5..bf34372 100755 --- a/main +++ b/main @@ -518,6 +518,7 @@ for dir in $(cd $outdir && find ./ -name figures); do mkdir -p output_report/$(dirname $dir) cp -r $outdir/$dir output_report/$(dirname $dir) done +mv output_report/fmriprep output_report/html #rename the parent directory to confirm to brainlife html output cat << EOF > product.json { From 54460b8d3eeff87af5f009c14cee2f1d758952b3 Mon Sep 17 00:00:00 2001 From: Soichi Hayashi Date: Fri, 15 May 2020 17:51:04 +0000 Subject: [PATCH 3/7] updated 1.5.10 removing "datatype" field from meta --- main | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/main b/main index bf34372..57884e7 100755 --- a/main +++ b/main @@ -159,7 +159,9 @@ if [[ $inFMRI != "null" ]] ; then name_FMRI=$bidsSubSesDir/func/$bidsSub name_FMRI=$(bids_namekeyvals $name_FMRI fmri.json "task acq ce dir rec run echo" $ses ) cp $inFMRI ${name_FMRI}_bold.nii.gz - jq -r ".meta" fmri.json > ${name_FMRI}_bold.json + #temporarily removing datataype field from meta as we used to copy all nifti headers + #into meta and it was colliding with BIDS datatype field + jq -r '.meta | del(.["datatype"])' fmri.json > ${name_FMRI}_bold.json bids_phaseencode_check ${name_FMRI}_bold.json fi @@ -405,7 +407,7 @@ export SINGULARITYENV_TEMPLATEFLOW_HOME=$PWD/templateflow echo $FREESURFER_LICENSE > license.txt time singularity exec -e \ - docker://poldracklab/fmriprep:1.5.5 \ + docker://poldracklab/fmriprep:1.5.10 \ /usr/local/miniconda/bin/fmriprep \ --notrack \ --resource-monitor \ @@ -422,12 +424,6 @@ time singularity exec -e \ --participant_label="$bidsSub" \ $bidsDir $outdir participant -#--fs-no-reconall \ -#--fs-subjects-dir="$outdir/freesurfer/$bidsSub" \ -#--fs-subjects-dir="$outdir/freesurfer" \ -#--output-spaces $output_space MNI152NLin2009cAsym \ -#-B $(pwd)/base.py:/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/bold/base.py \ - echo "done with fmriprep! - now organizing output" ##################################################################################### From 4429c887fd46847523900b7b419fc73a0a85e896 Mon Sep 17 00:00:00 2001 From: Soichi Hayashi Date: Fri, 15 May 2020 20:30:59 +0000 Subject: [PATCH 4/7] resetting freesurfer directory so fmriprep can write stuff to it --- main | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/main b/main index 57884e7..8564dbb 100755 --- a/main +++ b/main @@ -112,13 +112,8 @@ mkdir -p $bidsSubSesDir if [[ $inFSDIR != "null" ]] ; then mkdir -p $outdir/freesurfer - - # dont know if dir will be just inFSDIR or inFSDIR/output - if [[ -d $inFSDIR/output ]] ; then - cp -r $inFSDIR/output $outdir/freesurfer/$bidsSub - else - cp -r $inFSDIR $outdir/freesurfer/$bidsSub - fi + cp -r $inFSDIR $outdir/freesurfer/$bidsSub + chmod -R +rw $outdir/freesurfer fi ################################################################################ From e45e0ae23ff9fbf362c1dd2c146da1d2cd6fa1cf Mon Sep 17 00:00:00 2001 From: Soichi Hayashi Date: Sat, 16 May 2020 01:27:08 +0000 Subject: [PATCH 5/7] updated to use both task/TaskName or default task name --- main | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/main b/main index 8564dbb..19c54e4 100755 --- a/main +++ b/main @@ -150,15 +150,26 @@ fi if [[ $inFMRI != "null" ]] ; then mkdir -p $bidsSubSesDir/func jq '._inputs[] | select(.id == "fmri")' config.json > fmri.json - # fmri needs task in the filename to be defined! + + name_FMRI=$bidsSubSesDir/func/$bidsSub name_FMRI=$(bids_namekeyvals $name_FMRI fmri.json "task acq ce dir rec run echo" $ses ) cp $inFMRI ${name_FMRI}_bold.nii.gz + + # fmriprep needs task in the filename to be defined! + # let's use task, TaskName, and if neither is set, set it to unknown + task=$(jq .meta.task fmri.json) + if [ "$task" == null ]; then + task=$(jq .meta.TaskName fmri.json) + if [ "$task" == null ]; then + task="unknown" + fi + fi + #temporarily removing datataype field from meta as we used to copy all nifti headers #into meta and it was colliding with BIDS datatype field - jq -r '.meta | del(.["datatype"])' fmri.json > ${name_FMRI}_bold.json + jq -r '.meta | del(.["datatype"])' fmri.json | jq ".meta.task = \"$task\"" > ${name_FMRI}_bold.json bids_phaseencode_check ${name_FMRI}_bold.json - fi ################################################################################ # From 9a2c10c7129825a098e2e9086f8888be12d69e3c Mon Sep 17 00:00:00 2001 From: Soichi Hayashi Date: Sat, 16 May 2020 01:38:45 +0000 Subject: [PATCH 6/7] fixed where task is set --- main | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main b/main index 19c54e4..8068d8d 100755 --- a/main +++ b/main @@ -168,7 +168,7 @@ if [[ $inFMRI != "null" ]] ; then #temporarily removing datataype field from meta as we used to copy all nifti headers #into meta and it was colliding with BIDS datatype field - jq -r '.meta | del(.["datatype"])' fmri.json | jq ".meta.task = \"$task\"" > ${name_FMRI}_bold.json + jq -r '.meta | del(.["datatype"])' fmri.json | jq ".task = \"$task\"" > ${name_FMRI}_bold.json bids_phaseencode_check ${name_FMRI}_bold.json fi ################################################################################ From 9d4aada673b5adee5b02be0c490e98d3e7a1f5e7 Mon Sep 17 00:00:00 2001 From: Soichi Hayashi Date: Sat, 16 May 2020 02:21:33 +0000 Subject: [PATCH 7/7] fixed the way task/TaskName is pulled --- main | 51 +++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 37 insertions(+), 14 deletions(-) diff --git a/main b/main index 8068d8d..574c855 100755 --- a/main +++ b/main @@ -147,30 +147,53 @@ fi ################################################################################ # FMRI +#if [[ $inFMRI != "null" ]] ; then +# mkdir -p $bidsSubSesDir/func +# jq '._inputs[] | select(.id == "fmri")' config.json > fmri.json +# +# # fmriprep needs task in the filename to be defined! +# # let's use task, TaskName, and if neither is set, set it to unknown +# task=$(jq .meta.task fmri.json) +# if [ "$task" == null ]; then +# task=$(jq .meta.TaskName fmri.json) +# if [ "$task" == null ]; then +# task="unknown" +# fi +# fi +# +# #temporarily removing datataype field from meta as we used to copy all nifti headers +# #into meta and it was colliding with BIDS datatype field +# name_FMRI=$bidsSubSesDir/func/$bidsSub +# jq '.meta | del(.["datatype"])' fmri.json | jq ".task = \"$task\"" > ${name_FMRI}_bold.json +# echo "Wrote to ${name_FMRI}_bold.json" +# +# name_FMRI=$(bids_namekeyvals $name_FMRI ${name_FMRI}_bold.json "task acq ce dir rec run echo" $ses ) +# cp $inFMRI ${name_FMRI}_bold.nii.gz +# +# bids_phaseencode_check ${name_FMRI}_bold.json +#fi + if [[ $inFMRI != "null" ]] ; then mkdir -p $bidsSubSesDir/func - jq '._inputs[] | select(.id == "fmri")' config.json > fmri.json + jq '._inputs[] | select(.id == "fmri")' config.json > fmri.prep.json - - name_FMRI=$bidsSubSesDir/func/$bidsSub - name_FMRI=$(bids_namekeyvals $name_FMRI fmri.json "task acq ce dir rec run echo" $ses ) - cp $inFMRI ${name_FMRI}_bold.nii.gz - - # fmriprep needs task in the filename to be defined! - # let's use task, TaskName, and if neither is set, set it to unknown - task=$(jq .meta.task fmri.json) + # fmri needs task in the filename to be defined! + task=$(jq -r .meta.task fmri.prep.json) if [ "$task" == null ]; then - task=$(jq .meta.TaskName fmri.json) + task=$(jq -r .meta.TaskName fmri.prep.json) if [ "$task" == null ]; then task="unknown" fi fi + cat fmri.prep.json | jq ".meta.task = \"$task\"" > fmri.json - #temporarily removing datataype field from meta as we used to copy all nifti headers - #into meta and it was colliding with BIDS datatype field - jq -r '.meta | del(.["datatype"])' fmri.json | jq ".task = \"$task\"" > ${name_FMRI}_bold.json - bids_phaseencode_check ${name_FMRI}_bold.json + name_FMRI=$bidsSubSesDir/func/$bidsSub + name_FMRI=$(bids_namekeyvals $name_FMRI fmri.json "task acq ce dir rec run echo" $ses ) + cp $inFMRI ${name_FMRI}_bold.nii.gz + jq -r '.meta | del(.["datatype"])' fmri.json > ${name_FMRI}_bold.json + bids_phaseencode_check ${name_FMRI}_bold.json fi + ################################################################################ # # FMAP