Add connectoflow

tree_for_connectoflow.sh

@@ -0,0 +1,89 @@
+#!/usr/bin/env bash
+usage() { echo "$(basename $0) [-t tractoflow/results] [-n noddi/results] [-n setflow/results] [-w freewater_flow/results] [-f freesurfer_flow/results] [-o output]" 1>&2; exit 1; }
+
+while getopts "r:t:n:f:o:" args; do
+    case "${args}" in
+        t) t=${OPTARG};;
+        n) n=${OPTARG};;
+        s) s=${OPTARG};;
+        f) f=${OPTARG};;
+        o) o=${OPTARG};;
+        *) usage;;
+    esac
+done
+shift $((OPTIND-1))
+
+if [ -z "${f}" ] || [ -z "${t}" ] || [ -z "${o}" ]; then
+    usage
+fi
+
+echo "tractoflow results folder: ${t}"
+echo "noddi_flow results folder: ${n}"
+echo "freewater_flow results folder: ${w}"
+echo "freesurfer_flow results folder: ${f}"
+echo "setflow results folder: ${s}"
+echo "Output folder: ${o}"
+
+echo "Building tree for the following folders:"
+cd ${t}
+for i in *[!{Readme}];
+do
+    echo $i
+    mkdir -p $o/$i/metrics
+
+    # tractoflow metrics
+    ln -s $t/$i/DTI_Metrics/*fa.nii.gz $o/$i/metrics/fa.nii.gz
+    ln -s $t/$i/DTI_Metrics/*ad.nii.gz $o/$i/metrics/ad.nii.gz
+    ln -s $t/$i/DTI_Metrics/*md.nii.gz $o/$i/metrics/md.nii.gz
+    ln -s $t/$i/DTI_Metrics/*rd.nii.gz $o/$i/metrics/rd.nii.gz
+    ln -s $t/$i/FODF_Metrics/*afd_total.nii.gz $o/$i/metrics/afd_total.nii.gz
+    ln -s $t/$i/FODF_Metrics/*nufo.nii.gz $o/$i/metrics/nufo.nii.gz
+
+    # Peaks and FODF
+    ln -s $t/$i/FODF_Metrics/*peaks.nii.gz $o/$i/peaks.nii.gz
+    ln -s $t/$i/FODF_Metrics/*fodf.nii.gz $o/$i/fodf.nii.gz
+
+    # T1
+    ln -s $t/${i}/Register_T1/*__output0GenericAffine.mat $o/${i}/output0GenericAffine.mat
+    ln -s $t/${i}/Register_T1/*__t1_warped.nii.gz $o/${i}/1Warp.nii.gz
+    ln -s $t/${i}/Bet_T1/*__t1_bet.nii.gz $o/${i}/t1.nii.gz
+
+    # DWI
+    ln -s $t/${i}/Resample_DWI/*__dwi_resampled.nii.gz $o/${i}/dwi.nii.gz
+    ln -s $t/${i}/Eddy*/*__bval_eddy $o/${i}/dwi.bval
+    ln -s $t/${i}/Eddy*/*__dwi_eddy_corrected.bvec $o/${i}/dwi.bvec
+
+    if [[ ! -z "${s}" ]];
+    then
+      # Tracking from SET
+      ln -s ${s}/${i}/---------/*.trk ${o}/${i}/
+    else
+      # Tracking from Tractoflow
+      ln -s ${t}/${i}/*Tracking/*.trk ${o}/${i}/
+    fi
+
+    # noddi_flow metrics
+    if [[ ! -z "${n}" ]];
+    then
+      ln -s $n/$i/Compute_NODDI/*OD.nii.gz $o/$i/metrics/noddi_od.nii.gz
+      ln -s $n/$i/Compute_NODDI/*ISOVF.nii.gz $o/$i/metrics/noddi_isovf.nii.gz
+      ln -s $n/$i/Compute_NODDI/*ICVF.nii.gz $o/$i/metrics/noddi_icvf.nii.gz
+    fi
+
+    # freewater_flow metrics
+    if [[ ! -z "${w}" ]];
+    then
+      ln -s $w/$i/Compute_FreeWater/*FW.nii.gz $o/$i/metrics/freewater.nii.gz
+      ln -s $w/$i/FW_Corrected_Metrics/*fa.nii.gz $o/$i/metrics/FAt.nii.gz
+      ln -s $w/$i/FW_Corrected_Metrics/*ad.nii.gz $o/$i/metrics/ADt.nii.gz
+      ln -s $w/$i/FW_Corrected_Metrics/*rd.nii.gz $o/$i/metrics/RDt.nii.gz
+    fi
+
+    # freesurfer_flow template
+    if [[ ! -z "${f}" ]];
+    then
+      ln -s $f/$i/Generate_Atlases_FS_BN_GL_SF/atlas_brainnetome_v5.nii.gz $o/$i/labels.nii.gz
+      ln -s $f/$i/Generate_Atlases_FS_BN_GL_SF/atlas_brainnetome_v*_labels_list.txt $o/labels_list.txt
+    fi
+done
+echo "Done"