Merge pull request #156 from jhlegarreta/FixShellWMMeasurementLinuxCall

BUG: Fix WM diffusion measurement Python script call for Linux
SlicerDMRI · Sep 21, 2023 · e1b19a0 · e1b19a0
2 parents 3f74faf + 3c89a1b
commit e1b19a0
Showing 1 changed file with 20 additions and 4 deletions.
diff --git a/bin/wm_apply_ORG_atlas_to_subject.sh b/bin/wm_apply_ORG_atlas_to_subject.sh
@@ -389,22 +389,30 @@ fi
 
 if [ $DiffMeasure == 1 ]; then
 
+  os=$(uname)
+
+  if  [[ "$os" == 'Linux' ]]; then
+    measurement_cli_cmd=$SlicerPath" --launch "$FiberTractMeasurementsCLI
+  else
+    measurement_cli_cmd=$FiberTractMeasurementsCLI
+  fi
+
 	echo "<wm_apply_ORG_atlas_to_subject> Report diffusion measurements of fiber clusters."
 	if [ ! -f $SeparatedClustersFolder/diffusion_measurements_commissural.csv ]; then
 		wm_diffusion_measurements.py \
-			$SeparatedClustersFolder/tracts_commissural $SeparatedClustersFolder/diffusion_measurements_commissural.csv "$FiberTractMeasurementsCLI"
+			$SeparatedClustersFolder/tracts_commissural $SeparatedClustersFolder/diffusion_measurements_commissural.csv "$measurement_cli_cmd"
 	else
 		echo " - diffusion measurements of commissural clusters has been done."
 	fi
 	if [ ! -f $SeparatedClustersFolder/diffusion_measurements_left_hemisphere.csv ]; then
 		wm_diffusion_measurements.py \
-			$SeparatedClustersFolder/tracts_left_hemisphere $SeparatedClustersFolder/diffusion_measurements_left_hemisphere.csv "$FiberTractMeasurementsCLI"
+			$SeparatedClustersFolder/tracts_left_hemisphere $SeparatedClustersFolder/diffusion_measurements_left_hemisphere.csv "$measurement_cli_cmd"
 	else
 		echo " - diffusion measurements of left hemisphere clusters has been done."
 	fi
 	if [ ! -f $SeparatedClustersFolder/diffusion_measurements_right_hemisphere.csv ]; then
 		wm_diffusion_measurements.py \
-			$SeparatedClustersFolder/tracts_right_hemisphere $SeparatedClustersFolder/diffusion_measurements_right_hemisphere.csv "$FiberTractMeasurementsCLI"
+			$SeparatedClustersFolder/tracts_right_hemisphere $SeparatedClustersFolder/diffusion_measurements_right_hemisphere.csv "$measurement_cli_cmd"
 	else
 		echo " - diffusion measurements of right hemisphere clusters has been done."
 	fi
@@ -422,10 +430,18 @@ echo ""
 
 if [ $DiffMeasure == 1 ]; then
 
+  os=$(uname)
+
+  if  [[ "$os" == 'Linux' ]]; then
+    measurement_cli_cmd=$SlicerPath" --launch "$FiberTractMeasurementsCLI
+  else
+    measurement_cli_cmd=$FiberTractMeasurementsCLI
+  fi
+
 	echo "<wm_apply_ORG_atlas_to_subject> Report diffusion measurements of the anatomical tracts."
 	if [ ! -f $AnatomicalTractsFolder/diffusion_measurements_anatomical_tracts.csv ]; then
 		wm_diffusion_measurements.py \
-			$AnatomicalTractsFolder $AnatomicalTractsFolder/diffusion_measurements_anatomical_tracts.csv "$FiberTractMeasurementsCLI"
+			$AnatomicalTractsFolder $AnatomicalTractsFolder/diffusion_measurements_anatomical_tracts.csv "$measurement_cli_cmd"
 	else
 		echo " - diffusion measurements of anatomical tracts has been done."
 	fi