Merge pull request #336 from ariekahn/allow_res_tags

Allow for fmriprep resolution tags
PennLINC · May 22, 2020 · 4693f0f · 4693f0f
2 parents 39127b7 + cb7f2fa
commit 4693f0f
Show file tree

Hide file tree

Showing 2 changed files with 33 additions and 4 deletions.
diff --git a/modules/prestats/prestats.mod b/modules/prestats/prestats.mod
@@ -224,10 +224,25 @@ while (( ${#rem} > 0 ))
 
         routine @ getting data from fmriprep directory 
         exec_fsl immv ${intermediate} ${intermediate}_${cur}   
-        imgprt=${img1[sub]%_*_*_*}; conf="_desc-confounds_regressors.tsv"
+
+        # Check if we have a res- tag
+        # Added by recent versions of fmriprep
+        imgname=$(basename ${img1[sub]})
+        conf="_desc-confounds_regressors.tsv"
+        if [[ "$imgname" == *_res-* ]]; then
+           imgprt=${img1[sub]%_*_*_*_*}
+        else
+           imgprt=${img1[sub]%_*_*_*}
+        fi
         exec_sys cp ${imgprt}${conf} $out/prestats/${prefix}_fmriconf.tsv
+
         imgprt2=${img1[sub]%_*_*}; mskpart="_desc-brain_mask.nii.gz"
-        mask1=${imgprt2}${mskpart}; maskpart2=${mask1#*_*_*_*}
+        mask1=${imgprt2}${mskpart};
+        if [[ "$imgname" == *_res-* ]]; then
+           maskpart2=${mask1#*_*_*_*_*}
+        else
+           maskpart2=${mask1#*_*_*_*}
+        fi
         refpart="_boldref.nii.gz"; refvol=${imgprt2}${refpart}
 
         conf2="_desc-confounds_regressors.json"

diff --git a/modules/task/task.mod b/modules/task/task.mod
@@ -205,10 +205,24 @@ if (( ${task_fmriprep[cxt]} == 1 ))
 
          routine @ getting data from frmiprep directory 
 
-        imgprt=${img1[sub]%_*_*_*}; conf="_desc-confounds_regressors.tsv"
+        # Check if we have a res- tag
+        # Added by recent versions of fmriprep
+        imgname=$(basename ${img1[sub]})
+        conf="_desc-confounds_regressors.tsv"
+        if [[ "$imgname" == *_res-* ]]; then
+          imgprt=${img1[sub]%_*_*_*_*}
+        else
+          imgprt=${img1[sub]%_*_*_*}
+        fi
         exec_sys cp ${imgprt}${conf} ${out}/task/${prefix}_fmriconf.tsv
+
         imgprt2=${img1[sub]%_*_*}; mskpart="_desc-brain_mask.nii.gz"
-        mask1=${imgprt2}${mskpart}; maskpart2=${mask1#*_*_*_*}
+        mask1=${imgprt2}${mskpart};
+        if [[ "$imgname" == *_res-* ]]; then
+           maskpart2=${mask1#*_*_*_*_*}
+        else
+           maskpart2=${mask1#*_*_*_*}
+        fi
         refpart="_boldref.nii.gz"; refvol=${imgprt2}${refpart}
 
        output fmriprepconf  ${out}/task/${prefix}_fmriconf.tsv