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Updated cluster command in the script to fsl-cluster #14

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Updated cluster command in the script to fsl-cluster #14

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0d376e5
updated fsl-cluster command
Sawaiz8 May 2, 2026
f6974ff
removed b val file
Sawaiz8 May 2, 2026
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6 changes: 3 additions & 3 deletions alps.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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="${template}"; fi
Expand All @@ -559,7 +559,7 @@ then
fslmaths "${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_${template_abbreviation}.nii.gz"
Expand Down Expand Up @@ -703,7 +703,7 @@ then
assoc_L=${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

Expand Down