From 0d376e5c0520b137fb4c8b0ee582df13ad7c324c Mon Sep 17 00:00:00 2001
From: Sawaiz8 <sawaiz.nasim@gmail.com>
Date: Sat, 2 May 2026 18:17:42 +0500
Subject: [PATCH 1/2] updated fsl-cluster command

---
 alps.sh                 | 6 +++---
 bval/UCSF-PDGM_DTI.bval | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)
 create mode 100644 bval/UCSF-PDGM_DTI.bval

diff --git a/alps.sh b/alps.sh
index d48e291..88d6bd0 100644
--- a/alps.sh
+++ b/alps.sh
@@ -550,7 +550,7 @@ then
 				fslmaths "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz" -add "${outdir}/"$(basename "$(basename "$r" .gz)" .nii)"_in_${template_abbreviation}.nii.gz" "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
     			fi
       		done
-		cluster -t 1 -i "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz" -o "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
+		fsl-cluster -t 1 -i "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz" -o "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
 		#cp "${script_folder}/ROIs_JHU_ALPS/all_ROIs.nii.gz" "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
   	else #generate spheric ROIs in template space
    		if [ "${template}" == "0" ]; then template_roi=${FSLDIR}/data/atlases/JHU/JHU-ICBM-FA-1mm.nii.gz; template_abbreviation=JHU-FA; else template_roi="${template}"; fi
@@ -559,7 +559,7 @@ then
 		fslmaths "${template_roi}" -mul 0 -add 1 -roi 128 1 110 1 99 1 0 1 -kernel sphere $radius -fmean -bin "${outdir}/L_SLF_in_${template_abbreviation}.nii.gz" -odt float
 		fslmaths "${template_roi}" -mul 0 -add 1 -roi 52 1 110 1 99 1 0 1 -kernel sphere $radius -fmean -bin "${outdir}/R_SLF_in_${template_abbreviation}.nii.gz" -odt float
 		fslmaths "${outdir}/L_SCR_in_${template_abbreviation}.nii.gz" -add "${outdir}/R_SCR_in_${template_abbreviation}.nii.gz" -add "${outdir}/L_SLF_in_${template_abbreviation}.nii.gz" -add "${outdir}/R_SLF_in_${template_abbreviation}.nii.gz" -bin "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
-  		cluster -t 1 -i "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz" -o "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
+  		fsl-cluster -t 1 -i "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz" -o "${outdir}/all_ROIs_in_${template_abbreviation}.nii.gz"
     	fi
      	rois="${outdir}/L_SCR_in_${template_abbreviation}.nii.gz","${outdir}/R_SCR_in_${template_abbreviation}.nii.gz","${outdir}/L_SLF_in_${template_abbreviation}.nii.gz","${outdir}/R_SLF_in_${template_abbreviation}.nii.gz"
 	proj_L="${outdir}/L_SCR_in_${template_abbreviation}.nii.gz"
@@ -703,7 +703,7 @@ then
 			assoc_L=${outdir}/"$(basename "$(basename "$(basename "$(echo "${rois}" | cut -d ',' -f3)" .gz)" .nii)" _in_${template_abbreviation})"_native.nii.gz
    			assoc_R=${outdir}/"$(basename "$(basename "$(basename "$(echo "${rois}" | cut -d ',' -f4)" .gz)" .nii)" _in_${template_abbreviation})"_native.nii.gz
       			fslmaths "${proj_L}" -add "${proj_R}" -add "${assoc_L}" -add "${assoc_R}" -bin "${outdir}/all_ROIs_native.nii.gz"
-  			cluster -t 1 -i "${outdir}/all_ROIs_native.nii.gz" -o "${outdir}/all_ROIs_native.nii.gz"
+  			fsl-cluster -t 1 -i "${outdir}/all_ROIs_native.nii.gz" -o "${outdir}/all_ROIs_native.nii.gz"
 	  	#fi
 	fi
 
diff --git a/bval/UCSF-PDGM_DTI.bval b/bval/UCSF-PDGM_DTI.bval
new file mode 100644
index 0000000..d245e97
--- /dev/null
+++ b/bval/UCSF-PDGM_DTI.bval
@@ -0,0 +1 @@
+0 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000

From f6974ff1571ae59319510bc9ce3d0dac26aae62a Mon Sep 17 00:00:00 2001
From: Sawaiz8 <sawaiz.nasim@gmail.com>
Date: Sat, 2 May 2026 18:18:56 +0500
Subject: [PATCH 2/2] removed b val file

---
 bval/UCSF-PDGM_DTI.bval | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 bval/UCSF-PDGM_DTI.bval

diff --git a/bval/UCSF-PDGM_DTI.bval b/bval/UCSF-PDGM_DTI.bval
deleted file mode 100644
index d245e97..0000000
--- a/bval/UCSF-PDGM_DTI.bval
+++ /dev/null
@@ -1 +0,0 @@
-0 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000