ENH: Update getroicorrs for crest (#97)

* update paths and comments

* try to make run_getroicorrs recognized as octave with shebang

* fold in getroicorrs function and edits to match up variables

* update paths to find wrappers in docker container

* update comments

* add comment on how to output seedmaps

* changes to getroicorrs but note we won't call this anymore, it's folded into run_getroicorrs

* add run_getroicorrs test to circleci

* update run_getroicorrs files to take input of subject list and roilist

* remove hardcoding

* modify circleci to test roi-roi separately

* move the mv command

* change subnum to sub-num for bids

* remove dashes from filename

* try to fix paths for nuisance rois and add clobber since rois are running through roi loop

* add test for nuisance roi to fix access error in roi loop

* make fname more robust to text in subject label

Author: mwvoss

.circleci/config.yml

@@ -118,10 +118,10 @@ jobs:
             --t1_mask=/data/derivatives/bet/sub-01/anat/sub-01_desc-brainmask_T1w.nii.gz \
             --roiList=/data/derivatives/data/roi_list.txt \
             --compcor
-            mv /tmp/data/ds005/derivatives/rsOut /tmp/data/ds005/derivatives/rsOutCompcor
       - run:
           name: Check compcor outputs
           command: |
+            mv /tmp/data/ds005/derivatives/rsOut /tmp/data/ds005/derivatives/rsOutCompcor
             mkdir -p /tmp/ds005/test
             find /tmp/data/ds005/derivatives/rsOutCompcor -type f | sed s+/tmp/data/ds005/derivatives/rsOutCompcor++ | sort > /tmp/ds005/test/outputs-compcor.out
             diff /tmp/src/RestingState/.circleci/ds005_compcor.txt /tmp/ds005/test/outputs-compcor.out
@@ -131,6 +131,7 @@ jobs:
       - run:
           name: Test --compcor_global
           command: |
+            # run the original script
             docker run -ti --rm=false \
             -v /tmp/data/ds005:/data \
             hbclab/restingstate:latest \
@@ -139,10 +140,29 @@ jobs:
             --t1_mask=/data/derivatives/bet/sub-01/anat/sub-01_desc-brainmask_T1w.nii.gz \
             --roiList=/data/derivatives/data/roi_list.txt \
             --compcor_global
-            mv /tmp/data/ds005/derivatives/rsOut /tmp/data/ds005/derivatives/rsOutCompcorGlobal
+      - run:
+          name: Test roi-roi correlations
+          command: |
+            # inputs for run_getroicorrs
+            mkdir -p /tmp/ds005/test
+            echo "sub-01" > /tmp/ds005/test/subList.txt
+            echo -e "UIUC_VIS_lvis\nUIUC_VIS_rvis" > /tmp/ds005/test/roiList.txt
+
+            # get individual roi-roi correlations
+            docker run -it \
+            -v /tmp/data/ds005:/data \
+            -v /tmp:/tmp \
+            --entrypoint /opt/RestingState/run_getroicorrs_shell_wrapper.sh \
+            hbclab/restingstate:latest \
+            /data/derivatives/rsOut/ \
+            /tmp/ds005/test/subList.txt \
+            /tmp/ds005/test/roiList.txt
       - run:
           name: Check compcor_global outputs
           command: |
+            # move rsOut to it's own directory
+            mv /tmp/data/ds005/derivatives/rsOut /tmp/data/ds005/derivatives/rsOutCompcorGlobal
+
             mkdir -p /tmp/ds005/test
             find /tmp/data/ds005/derivatives/rsOutCompcorGlobal -type f | sed s+/tmp/data/ds005/derivatives/rsOutCompcorGlobal++ | sort > /tmp/ds005/test/outputs-compcor_global.out
             diff /tmp/src/RestingState/.circleci/ds005_compcor_global.txt /tmp/ds005/test/outputs-compcor_global.out

.circleci/ds005_compcor_global.txt

@@ -20,6 +20,9 @@
 /anat/sub-01/tissueSeg/T1_seg_1.nii.gz
 /anat/sub-01/tissueSeg/T1_seg_2.nii.gz
 /anat/sub-01/tissueSeg/T1_seg.nii.gz
+/roicorrs/roi-roi_corr.csv
+/roicorrs/sub-01.mat
+/roicorrs/subject_roi-pair_corr.csv
 /sub-01/3dTqual.png
 /sub-01/analysisResults.html
 /sub-01/AntNoise_Mean.par

getroicorrs.m

@@ -542,6 +542,7 @@ clobber "${epiDataFiltReg}" &&\
 clobber "${rsOut}"/motionScrub/"$(basename "${epiDataFiltReg/.nii/_ms.nii}")" &&\
 "${scriptdir}"/motionScrub.sh --epi="${epiDataFiltReg}"
 
+# add --seedmaps option if you want to get 3D seed-to-voxel fishers correlation map
 "${scriptdir}"/seedVoxelCorrelation.sh \
 --epi="${epiDataFiltReg}" \
 --motionscrub \

processRestingState_bids_wrapper.sh

@@ -365,10 +365,19 @@ do
     fslmeants -i "$epiData" -o "$outDir"/rois/mean_"${roiName}"_ts.txt -m "$outDir"/rois/"${roiName}"_native.nii.gz --eig --order=5
   elif [[ "${compcor_globalFlag}" -eq 1 ]]; then
     # mean for global
-    fslmeants -i "$epiData" -o "$outDir"/rois/mean_global_ts.txt -m "$outDir"/rois/global_native.nii.gz
+    clobber "$outDir"/rois/mean_global_ts.txt &&\
+      if [ -f "$outDir"/rois/global_native.nii.gz ]; then
+        fslmeants -i "$epiData" -o "$outDir"/rois/mean_global_ts.txt -m "$outDir"/rois/global_native.nii.gz
+      fi
     # eigenvariates for WM and CSF
-    fslmeants -i "$epiData" -o "$outDir"/rois/mean_CSF_pve_to_RS_thresh_ts.txt -m "$outDir"/rois/CSF_pve_to_RS_thresh_native.nii.gz --eig --order=5
-    fslmeants -i "$epiData" -o "$outDir"/rois/mean_WM_pve_to_RS_thresh_ero_ts.txt -m "$outDir"/rois/WM_pve_to_RS_thresh_ero_native.nii.gz --eig --order=5
+    clobber "$outDir"/rois/mean_CSF_pve_to_RS_thresh_ts.txt &&\
+      if [ -f "$outDir"/rois/CSF_pve_to_RS_thresh_native.nii.gz ]; then
+        fslmeants -i "$epiData" -o "$outDir"/rois/mean_CSF_pve_to_RS_thresh_ts.txt -m "$outDir"/rois/CSF_pve_to_RS_thresh_native.nii.gz --eig --order=5
+      fi
+    clobber "$outDir"/rois/mean_WM_pve_to_RS_thresh_ero_ts.txt &&\
+      if [ -f "$outDir"/rois/WM_pve_to_RS_thresh_ero_native.nii.gz ]; then
+        fslmeants -i "$epiData" -o "$outDir"/rois/mean_WM_pve_to_RS_thresh_ero_ts.txt -m "$outDir"/rois/WM_pve_to_RS_thresh_ero_native.nii.gz --eig --order=5
+      fi
   else
     clobber "$outDir"/rois/mean_"${roiName}"_ts.txt &&\
     fslmeants -i "$epiData" -o "$outDir"/rois/mean_"${roiName}"_ts.txt -m "$outDir"/rois/"${roiName}"_native.nii.gz