Merge pull request #321 from a3sha2/master

alff with res4d from task
PennLINC · Mar 21, 2020 · 2c47141 · 2c47141
2 parents 6d36d8f + ef060dd
commit 2c47141
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Showing 4 changed files with 24 additions and 13 deletions.
diff --git a/designs/anat_jlf_complete.dsn b/designs/anat_jlf_complete.dsn
@@ -74,11 +74,11 @@ gmd_cleanup[2]=1
 ###################################################################
 
 jlf_extract[3]=1 
-jlf_keep_warps[3]=1
+jlf_keep_warps[3]=0
 jlf_quick[3]=0
 jlf_cohort[3]=Younger24
 jlf_ncpu[3]=2
-jlf_parallel[3]=1
+jlf_parallel[3]=sge
 jlf_rerun[3]=0
 jlf_cleanup[3]=1
 

diff --git a/modules/alff/alff.mod b/modules/alff/alff.mod
@@ -94,12 +94,19 @@ smooth_spatial                --SIGNPOST=${signpost}              \
                               --INPUT=${uncensored[sub]}           \
                               --USAN=${alff_usan[cxt]}            \
                               --USPACE=${alff_usan_space[cxt]}
-else
+elif is_image ${denoised[sub]} ; then 
 smooth_spatial                --SIGNPOST=${signpost}              \
                               --FILTER=alff_sptf[cxt]             \
                               --INPUT=${denoised[sub]}           \
                               --USAN=${alff_usan[cxt]}            \
                               --USPACE=${alff_usan_space[cxt]}
+elif is_image ${res4d[sub]} ; then 
+smooth_spatial                --SIGNPOST=${signpost}              \
+                              --FILTER=alff_sptf[cxt]             \
+                              --INPUT=${res4d[sub]}           \
+                              --USAN=${alff_usan[cxt]}            \
+                              --USPACE=${alff_usan_space[cxt]}
+
 fi
 
 routine_end

diff --git a/modules/jlf/jlf.mod b/modules/jlf/jlf.mod
@@ -113,16 +113,16 @@ if ! is_image ${labels[cxt]} \
    done
 
    subroutine                 @1.5  Configuring parallelisation
-   case ${jlf_parallel[cxt]} in
-   sge)
-      define jlf_parallel  1
-      ;;
-   pbs)
-      define jlf_parallel  4
-      ;;
-   *)
-      define jlf_parallel  0
-   esac
+   #case ${jlf_parallel[cxt]} in
+   #sge)
+      #define jlf_parallel  1
+      #;;
+   #pbs)
+     # define jlf_parallel  4
+      #;;
+   #*)
+     # define jlf_parallel  0
+   #esac
 echo ${img[sub]} 2
    subroutine                 @1.6a Executing joint label fusion routine
    subroutine                 @1.6b Delegating control to antsJointLabelFusion

diff --git a/modules/task/task.mod b/modules/task/task.mod
@@ -1089,6 +1089,10 @@ if [[ -d ${featout} ]]
       done
    fi
 
+    res4d=$(ls -f ${featout}/stats/*res4d.nii.gz )
+
+    output  res4d ${res4d}
+
    # add post surface processing here if  there is fmriprep 
 
    surf=$( ls -f $strucn/anat/*hemi-L_inflated.surf.gii 2>/dev/null )