Ic aroma

clean.sh

@@ -1,19 +1,20 @@
-rm -rf anat 
-rm -rf anat_mask 
-rm -rf bold_img 
+rm -rf anat
+rm -rf anat_mask
+rm -rf bold_img
 rm -rf bold_mask
-rm -f fmap.json 
-rm -f fmri.json 
-rm -rf fmripinput 
-rm -rf out 
-rm -rf workdir 
-rm -f license.txt 
-rm -f multi_proc.yml 
-rm -f nohup.out 
+rm -f fmap.json
+rm -f fmri.json
+rm -rf fmripinput
+rm -rf out
+rm -rf workdir
+rm -f license.txt
+rm -f multi_proc.yml
+rm -f nohup.out
 rm -rf output_report
-rm -f product.json 
-rm -rf regress 
-rm -f t1w.json 
-rm -f t2w.json 
-rm -rf templateflow 
+rm -f product.json
+rm -rf regress
+rm -rf aroma  
+rm -f t1w.json
+rm -f t2w.json
+rm -rf templateflow
 rm -rf bids

fmriprep2bl.sh

@@ -12,7 +12,8 @@ product=""
 
 # get basename for fmri output
 sub=$(jq -r '._inputs[] | select(.id == "fmri") | .meta.subject' config.json)
-oDir=$outdir/fmriprep/sub-$sub
+# oDir=$outdir/fmriprep/sub-$sub
+oDir=$outdir/sub-$sub
 ses=$(jq -r '._inputs[] | select(.id == "fmri") | .meta.session' config.json)
 [ "$ses" != "null" ] && oDir=$oDir/ses-$ses
 
@@ -22,6 +23,12 @@ regressors_tsv=$(find $oDir/func -name "*_desc-confounds_timeseries.tsv")
 regressors_json=$(find $oDir/func -name "*_desc-confounds_timeseries.json")
 [[ -f $regressors_json ]] && cp $regressors_json regress/regressors.json
 
+# ADDITION vvvv
+mkdir -p aroma
+aroma_csv=$(find $oDir/func -name "*AROMAnoiseICs.csv")
+[[ -f $aroma_csv ]] && cp $aroma_csv aroma/aroma.csv
+# ADDITION ^^^^
+
 # need to check if we have surface or volume output,
 # this will match for fsaverage, fsaverage5, ...
 space=$(jq -r .space config.json)
@@ -47,14 +54,20 @@ if [[ $space =~ 'fsaverage' ]] || [[ $space == 'fsnative' ]] ; then
 
 else # else its a volume(bold) output
 
-    bold_json=$(find $oDir/func -name "*_desc-preproc_bold.json")
+    # CHANGE HERE vvvv
+    # bold_json=$(find $oDir/func -name "*_desc-preproc_bold.json")
+    bold_json=$(find $oDir/func -name "*_desc-smoothAROMAnonaggr_bold.json")
+    # CHANGE HERE ^^^^
     time singularity exec -e docker://brainlife/python:2.7.16 python ./merge_json.py -f1 config.json -f2 $bold_json -id_in fmri -out tmp.json
     product="\"bold_img\": {\"meta\": $(cat tmp.json), \"space\": \"$space\", \"tags\": [ \"space-$space\" ]}, $product"
 
     # get the preproc fmri vol
     mkdir -p bold_img
-    #sub-A00008326_ses-DS2_task-rest_acq-645_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
-    ln -sf ../$(find $oDir/func -name "*_space-${space}_*desc-preproc_bold.nii.gz") bold_img/bold.nii.gz
+
+    # CHANGE HERE vvvv
+    # ln -sf ../$(find $oDir/func -name "*_space-${space}_*desc-preproc_bold.nii.gz") bold_img/bold.nii.gz
+    ln -sf ../$(find $oDir/func -name "*_space-${space}_*desc-smoothAROMAnonaggr_bold.nii.gz") bold_img/bold.nii.gz
+    # CHANGE HERE ^^^^
 
     # get the preproc fmri volmask
     mkdir -p bold_mask
@@ -66,7 +79,8 @@ fi
 # TODO - should we output all output spaces?
 mkdir -p anat anat_mask
 sub=$(jq -r '._inputs[] | select(.id == "t1w") | .meta.subject' config.json)
-oDir=$outdir/fmriprep/sub-$sub
+# oDir=$outdir/fmriprep/sub-$sub
+oDir=$outdir/sub-$sub
 ses=$(jq -r '._inputs[] | select(.id == "t1w") | .meta.session' config.json)
 [ "$ses" != "null" ] && oDir=$oDir/ses-$ses
 #anat
@@ -91,11 +105,12 @@ for dir in $(cd $outdir && find ./ -name "figures"); do
     cp -r $outdir/$dir output_report/$(dirname $dir)
 done
 #rename the parent directory to confirm to brainlife html output
-mv output_report/fmriprep output_report/html
+# mv output_report/fmriprep output_report/html # this line is throwing error - e.b.
+# mv output_report output_report/html
 
 ### aparcaseg parcellation datatype
 mkdir -p parcellation
-labelsTsv=$outdir/fmriprep/desc-aparcaseg_dseg.tsv
+labelsTsv=$outdir/desc-aparcaseg_dseg.tsv
 cp ${labelsTsv} ./labels.tsv
 #oDir=$outdir/fmriprep/sub-$sub
 ln -sf ../$(find $oDir/anat -name "*_desc-aparcaseg_dseg.nii.gz" -not -name "*space*") parcellation/parc.nii.gz

main

@@ -28,7 +28,7 @@ fi
 
 outdir=out
 
-#we should avoid using lustre filesystem as workdir on Expsnse@SDSC, 
+#we should avoid using lustre filesystem as workdir on Expsnse@SDSC,
 #admin told me that it's causing high IOP
 WORKDIRNAME=work
 if [ -d "/scratch/$USER/job_$SLURM_JOB_ID" ]; then