Merge branch 'master' of github.com:PennBBL/xcpEngine

PennLINC · Jan 17, 2019 · c448ee3 · c448ee3
2 parents c89ef01 + 98941e6
commit c448ee3
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Showing 2 changed files with 18 additions and 18 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -6,6 +6,7 @@ RUN sed -i '$iexport PATH=$PATH:$XCPEDIR' $ND_ENTRYPOINT
 
 ADD . /xcpEngine
 
+
 RUN bash -c \
     'cd  /xcpEngine \
     && wget -nv https://upenn.box.com/shared/static/i30llenk6s37kv8nkqxgulwylaxp928g.xz \

diff --git a/modules/prestats/prestats.mod b/modules/prestats/prestats.mod
@@ -234,18 +234,18 @@ while (( ${#rem} > 0 ))
 
                output referenceVolume  ${out}/prestats/${prefix}_referenceVolume.nii.gz
 
-               rm -rf /tmp/imgmask.nii.gz
+
                exec_afni 3dresample -orient ${template_orientation} \
-               -inset ${mask1} -prefix  /tmp/imgmask.nii.gz
-
-               rm -rf /tmp/structmask.nii.gz
+               -inset ${mask1} -prefix ${prefix}_imgmask.nii.gz
+
                exec_afni 3dresample -master ${out}/prestats/${prefix}_referenceVolume.nii.gz \
-                  -inset ${structmask}  -prefix /tmp/structmask.nii.gz
+                  -inset ${structmask}  -prefix ${prefix}_structmask.nii.gz
 
-               exec_fsl fslmaths /tmp/imgmask.nii.gz -mul /tmp/structmask.nii.gz \
+               exec_fsl fslmaths ${prefix}_imgmask.nii.gz -mul ${prefix}_structmask.nii.gz \
                       ${out}/prestats/${prefix}_mask.nii.gz
                 output mask  ${out}/prestats/${prefix}_mask.nii.gz
-
+                rm ${prefix}_structmask.nii.gz
+                rm ${prefix}_imgmask.nii.gz
 
                exec_afni 3dresample -master ${mask[cxt]} \
                    -inset ${segmentation[sub]}  \
@@ -345,16 +345,15 @@ while (( ${#rem} > 0 ))
 
                        subroutine        @  generate mask and referenceVolumeBrain 
 
-
-                       rm -rf /tmp/structmask.nii.gz
+
                        exec_afni 3dresample -master ${referenceVolume[cxt]} \
-                          -inset ${structmask}  -prefix /tmp/structmask.nii.gz
+                          -inset ${structmask}  -prefix ${prefix}_structmask.nii.gz
 
-                      exec_fsl fslmaths ${mask1} -mul /tmp/structmask.nii.gz \
+                      exec_fsl fslmaths ${mask1} -mul ${prefix}_structmask.nii.gz \
                       ${out}/prestats/${prefix}_mask.nii.gz
 
                       output mask  ${out}/prestats/${prefix}_mask.nii.gz
-
+                      rm ${prefix}_structmask.nii.gz
 
                       exec_fsl fslmaths  ${mask[cxt]} -mul ${referenceVolume[cxt]} \
                           ${out}/prestats/${prefix}_referenceVolumeBrain.nii.gz 
@@ -407,17 +406,17 @@ while (( ${#rem} > 0 ))
                        -prefix  ${out}/prestats/${prefix}_referenceVolume.nii.gz
                     output referenceVolume  ${out}/prestats/${prefix}_referenceVolume.nii.gz
 
-                   rm -rf /tmp/imgmask.nii.gz
+
                    exec_afni 3dresample -orient ${template_orientation} \
-                         -inset ${mask1} -prefix  /tmp/imgmask.nii.gz
+                    -inset ${mask1} -prefix  ${prefix}_imgmask.nii.gz
 
-                   rm -rf /tmp/structmask.nii.gz
+
                    exec_afni 3dresample -master ${referenceVolume[cxt]} \
-                    -inset ${structmask} -prefix /tmp/structmask.nii.gz
+                     -inset ${structmask} -prefix ${prefix}_structmask.nii.gz
 
-                   exec_fsl fslmaths  /tmp/imgmask.nii.gz -mul /tmp/structmask.nii.gz ${out}/prestats/${prefix}_mask.nii.gz
+                   exec_fsl fslmaths  ${prefix}_imgmask.nii.gz -mul ${prefix}_structmask.nii.gz ${out}/prestats/${prefix}_mask.nii.gz
                    output mask  ${out}/prestats/${prefix}_mask.nii.gz
-
+                    rm ${prefix}_structmask.nii.gz ${prefix}_imgmask.nii.gz
 
                   exec_afni 3dresample -master ${referenceVolume[cxt]} -inset ${segmentation1}   \
                          -prefix ${out}/prestats/${prefix}_segmentation.nii.gz