From 19842ec7ec91ea838db763c00e81c5c4c40991b0 Mon Sep 17 00:00:00 2001
From: Eva Bacas <ENB30@pitt.edu>
Date: Mon, 3 Oct 2022 13:53:53 -0400
Subject: [PATCH 01/11] modified bold output; added aroma IC csv

---
 fmriprep2bl.sh | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/fmriprep2bl.sh b/fmriprep2bl.sh
index 11f63c7..6a18d38 100755
--- a/fmriprep2bl.sh
+++ b/fmriprep2bl.sh
@@ -22,6 +22,12 @@ 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_ic
+aroma_csv=$(find $oDir/func -name "*AROMAnoiseICs.csv")
+[[ -f $aroma_csv ]] && cp $aroma_csv aroma_ic/aroma_csv
+# ADDITION ^^^^
+
 # need to check if we have surface or volume output,
 # this will match for fsaverage, fsaverage5, ...
 space=$(jq -r .space config.json)
@@ -47,14 +53,20 @@ 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

From fa81328ee2802b29f2b71bc843c5167e16ed4427 Mon Sep 17 00:00:00 2001
From: Eva Bacas <ENB30@pitt.edu>
Date: Mon, 3 Oct 2022 14:48:06 -0400
Subject: [PATCH 02/11] small edits

---
 fmriprep2bl.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/fmriprep2bl.sh b/fmriprep2bl.sh
index 6a18d38..9b07e05 100755
--- a/fmriprep2bl.sh
+++ b/fmriprep2bl.sh
@@ -23,9 +23,8 @@ regressors_json=$(find $oDir/func -name "*_desc-confounds_timeseries.json")
 [[ -f $regressors_json ]] && cp $regressors_json regress/regressors.json
 
 # ADDITION vvvv
-mkdir -p aroma_ic
 aroma_csv=$(find $oDir/func -name "*AROMAnoiseICs.csv")
-[[ -f $aroma_csv ]] && cp $aroma_csv aroma_ic/aroma_csv
+[[ -f $aroma_csv ]] && cp $aroma_csv regressors/aroma_csv
 # ADDITION ^^^^
 
 # need to check if we have surface or volume output,

From a633229f77ad625a9d543bf7ac4c1e65ce2c2eae Mon Sep 17 00:00:00 2001
From: eva bacas <ENB30@pitt.edu>
Date: Tue, 11 Oct 2022 11:06:52 -0400
Subject: [PATCH 03/11] fixed aroma regressor output

---
 fmriprep2bl.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep2bl.sh b/fmriprep2bl.sh
index 9b07e05..334bd57 100755
--- a/fmriprep2bl.sh
+++ b/fmriprep2bl.sh
@@ -24,7 +24,7 @@ regressors_json=$(find $oDir/func -name "*_desc-confounds_timeseries.json")
 
 # ADDITION vvvv
 aroma_csv=$(find $oDir/func -name "*AROMAnoiseICs.csv")
-[[ -f $aroma_csv ]] && cp $aroma_csv regressors/aroma_csv
+[[ -f $aroma_csv ]] && cp $aroma_csv regress/aroma.csv
 # ADDITION ^^^^
 
 # need to check if we have surface or volume output,

From 914977a1e921306ef9c3bd632fd97fe270cce323 Mon Sep 17 00:00:00 2001
From: eva bacas <ENB30@pitt.edu>
Date: Thu, 20 Oct 2022 11:27:27 -0400
Subject: [PATCH 04/11] actually fixed

---
 fmriprep2bl.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/fmriprep2bl.sh b/fmriprep2bl.sh
index 334bd57..d8d063f 100755
--- a/fmriprep2bl.sh
+++ b/fmriprep2bl.sh
@@ -23,8 +23,9 @@ 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 regress/aroma.csv
+[[ -f $aroma_csv ]] && cp $aroma_csv aroma/aroma.csv
 # ADDITION ^^^^
 
 # need to check if we have surface or volume output,

From e1e5f7dcc30b1aca41c862c88b335d16cf8cf6ad Mon Sep 17 00:00:00 2001
From: Eva Bacas <ENB30@pitt.edu>
Date: Mon, 24 Oct 2022 14:28:01 -0400
Subject: [PATCH 05/11] commented out weird = line

---
 clean.sh | 33 +++++++++++++++++----------------
 main     |  4 ++--
 2 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/clean.sh b/clean.sh
index 324bbd5..d6522bc 100755
--- a/clean.sh
+++ b/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
diff --git a/main b/main
index 1b75fa9..9e57ac5 100755
--- a/main
+++ b/main
@@ -19,7 +19,7 @@ EOF
 
 #source bids_funcs.sh
 
-=======
+# ======= # this threw an error so i'm taking it out -e.b.
 WORKDIRNAME=work
 if [ -d "/scratch/$USER/job_$SLURM_JOB_ID" ]; then
     echo "using NVMe directory"
@@ -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

From beac8e6014d4c4b9a5f42e75c0e9017219801ad5 Mon Sep 17 00:00:00 2001
From: Eva Bacas <ENB30@pitt.edu>
Date: Thu, 27 Oct 2022 12:54:48 -0400
Subject: [PATCH 06/11] fixed oDir

---
 fmriprep2bl.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/fmriprep2bl.sh b/fmriprep2bl.sh
index d8d063f..ecd9a28 100755
--- a/fmriprep2bl.sh
+++ b/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
 
@@ -78,7 +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

From 037968cf2da1536462ed5518068d0b0f2ea9f006 Mon Sep 17 00:00:00 2001
From: Brad Caron <bacaron245@gmail.com>
Date: Wed, 2 Nov 2022 11:12:58 -0500
Subject: [PATCH 07/11] Update main

This will fix the issue with 21.0.1 where the default behavior of output_layout changed, causing fMRIPRep to look for input freesurfers in the incorrect location.
---
 main | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/main b/main
index 9e57ac5..bc14a4d 100755
--- a/main
+++ b/main
@@ -95,6 +95,9 @@ if [[ $inFSDIR != "null" ]] ; then
     sub=$(jq -r '._inputs[] | select(.id == "t1w") | .meta.subject' config.json)
     cp -rH $inFSDIR $outdir/freesurfer/sub-$sub
     chmod -R +rw $outdir/freesurfer
+    fs_dir_line=$(eval "echo --fs-subjects-dir \${outdir}/freesurfer")
+else
+    fs_dir_line=''
 fi
 
 # avoid templateflow problems on HPC's running singularity
@@ -124,6 +127,7 @@ time singularity exec -e \
     --use-syn-sdc \
     $aroma \
     $skipbidsvalidation \
+    $fs_dir_line \
     --skull-strip-template=NKI \
     --work-dir=$WORKDIRNAME \
     --fs-license-file=license.txt \

From d0cbd84570160cb6f0eacc4f57ac5d544afbd393 Mon Sep 17 00:00:00 2001
From: Eva Bacas <ENB30@pitt.edu>
Date: Thu, 3 Nov 2022 11:04:17 -0400
Subject: [PATCH 08/11] pulled edits to main

---
 main | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/main b/main
index 9e57ac5..81416a2 100755
--- a/main
+++ b/main
@@ -19,7 +19,7 @@ EOF
 
 #source bids_funcs.sh
 
-# ======= # this threw an error so i'm taking it out -e.b.
+#=======
 WORKDIRNAME=work
 if [ -d "/scratch/$USER/job_$SLURM_JOB_ID" ]; then
     echo "using NVMe directory"
@@ -95,6 +95,9 @@ if [[ $inFSDIR != "null" ]] ; then
     sub=$(jq -r '._inputs[] | select(.id == "t1w") | .meta.subject' config.json)
     cp -rH $inFSDIR $outdir/freesurfer/sub-$sub
     chmod -R +rw $outdir/freesurfer
+    fs_dir_line=$(eval "echo --fs-subjects-dir \${outdir}/freesurfer")
+else
+    fs_dir_line=''
 fi
 
 # avoid templateflow problems on HPC's running singularity
@@ -124,6 +127,7 @@ time singularity exec -e \
     --use-syn-sdc \
     $aroma \
     $skipbidsvalidation \
+    $fs_dir_line \
     --skull-strip-template=NKI \
     --work-dir=$WORKDIRNAME \
     --fs-license-file=license.txt \

From 0ead11b6247477bb0664edf06cdfc80e43cc5414 Mon Sep 17 00:00:00 2001
From: Eva Bacas <ENB30@pitt.edu>
Date: Mon, 7 Nov 2022 10:23:06 -0500
Subject: [PATCH 09/11] fixed file save error

---
 fmriprep2bl.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/fmriprep2bl.sh b/fmriprep2bl.sh
index ecd9a28..ba10f0c 100755
--- a/fmriprep2bl.sh
+++ b/fmriprep2bl.sh
@@ -105,7 +105,8 @@ 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

From 461dc4315f4c5369eb0a45a968be90813cdf5a1f Mon Sep 17 00:00:00 2001
From: Eva Bacas <ENB30@pitt.edu>
Date: Mon, 7 Nov 2022 14:20:21 -0500
Subject: [PATCH 10/11] please work

---
 fmriprep2bl.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep2bl.sh b/fmriprep2bl.sh
index ba10f0c..965061c 100755
--- a/fmriprep2bl.sh
+++ b/fmriprep2bl.sh
@@ -106,7 +106,7 @@ for dir in $(cd $outdir && find ./ -name "figures"); do
 done
 #rename the parent directory to confirm to brainlife html output
 # mv output_report/fmriprep output_report/html # this line is throwing error - e.b.
-mv output_report output_report/html
+# mv output_report output_report/html
 
 ### aparcaseg parcellation datatype
 mkdir -p parcellation

From 87c213e0cdc0ce4fd7496602bb565750b59ebf76 Mon Sep 17 00:00:00 2001
From: Eva Bacas <ENB30@pitt.edu>
Date: Tue, 8 Nov 2022 09:14:00 -0500
Subject: [PATCH 11/11] if it isn't fixed this time i'm throwing myself
 directly into the sun

---
 fmriprep2bl.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep2bl.sh b/fmriprep2bl.sh
index 965061c..cc2367a 100755
--- a/fmriprep2bl.sh
+++ b/fmriprep2bl.sh
@@ -110,7 +110,7 @@ done
 
 ### 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