freesurfer_hippo_subfields_jobs.txt

+segmentHA_T1.sh HP01
+segmentHA_T1.sh HP02
+segmentHA_T1.sh HP03
+segmentHA_T1.sh HP12
+segmentHA_T1.sh HP04
+segmentHA_T1.sh HP11
+segmentHA_T1.sh HP05
+segmentHA_T1.sh HP06
+segmentHA_T1.sh HP07
+segmentHA_T1.sh HP17
+segmentHA_T1.sh HP08
+segmentHA_T1.sh HP14
+segmentHA_T1.sh HP09
+segmentHA_T1.sh HP10
+segmentHA_T1.sh HP20
+segmentHA_T1.sh HP16
+segmentHA_T1.sh HP21
+segmentHA_T1.sh HP19
+segmentHA_T1.sh HP22
+segmentHA_T1.sh HP23
+segmentHA_T1.sh HP24
+segmentHA_T1.sh HP25
+segmentHA_T1.sh HP26
+segmentHA_T1.sh HP27
+segmentHA_T1.sh HP28
+segmentHA_T1.sh HP15
+segmentHA_T1.sh HP29
+segmentHA_T1.sh HP30
+segmentHA_T1.sh HP18

freesurfer_hipposubfield_collapseSubfields.sh

+seg_dir="/vols/Data/psychiatry/BHC/SUBPROJECTS/BHC_hippo_seg/freesurfer_hipposubfield/post_processing"
+
+for dir in $seg_dir/HP*; do
+    cd $dir 
+    echo "Checking ${dir##*/}..."
+
+    if ! [ -f "rh_hipp.nii.gz" ]; then
+        input_left_img="lh.hippoAmygLabels-T1-AN.v21.FSvoxelSpace.mgz"
+        input_right_img="rh.hippoAmygLabels-T1-AN.v21.FSvoxelSpace.mgz"
+
+        mri_binarize --i $input_left_img --match 203 211 212 215 226 233 234 235 236 237 238 239 240 241 242 243 244 245 246 --o lh_hipp.mgz
+        mri_binarize --i $input_right_img --match 203 211 212 215 226 233 234 235 236 237 238 239 240 241 242 243 244 245 246 --o rh_hipp.mgz
+
+        mri_convert lh_hipp.mgz lh_hipp.nii.gz
+        mri_convert rh_hipp.mgz rh_hipp.nii.gz
+
+        echo "${dir##*/}: Finished"
+    else
+        echo "${dir##*/}: outputs already exist..proceeding to next subject"
+    fi
+done
+

freesurfer_hipposubfield_map_segm.sh

+seg_dir="/vols/Data/psychiatry/BHC/SUBPROJECTS/BHC_hippo_seg/freesurfer_hipposubfield/post_processing"
+ref_dir="/vols/Data/psychiatry/BHC/SUBPROJECTS/BHC_hippo_seg"
+# Transform masks
+for dir in $seg_dir/HP*; do
+    cd $dir
+    echo "Checking ${dir##*/}..."
+
+       if ! [ -f "${dir##*/}_R_hippocampus_ToBrain_binarised.nii.gz" ]; then
+
+
+          input_left_img="lh_hipp.nii.gz"
+          input_right_img="rh_hipp.nii.gz"
+          ref_img=$ref_dir/${dir##*/}/${dir##*/}_T1_brain.nii.gz
+
+          # Apply FLIRT with rigid body transformations to map them on ground truth image
+          flirt -in $input_left_img -ref $ref_img -applyxfm -usesqform -out T1_orig_L_hippocampus_ToBrain.nii.gz
+          flirt -in $input_right_img -ref $ref_img -applyxfm -usesqform -out T1_orig_R_hippocampus_ToBrain.nii.gz
+
+          # Binarize them to create masks for further comparison
+          fslmaths T1_orig_L_hippocampus_ToBrain.nii.gz -thr 0.5 -bin T1_orig_L_hippocampus_ToBrain_binarised.nii.gz
+          fslmaths T1_orig_R_hippocampus_ToBrain.nii.gz -thr 0.5 -bin T1_orig_R_hippocampus_ToBrain_binarised.nii.gz
+
+          echo "${dir##*/}: Finished"
+       else
+          echo "${dir##*/}: outputs already exist..proceeding to next step"
+       fi
+done
\ No newline at end of file

freesurfer_hipposubfield_map_segs_groundtruth.sh

+seg_dir="/vols/Data/psychiatry/BHC/SUBPROJECTS/BHC_hippo_seg/freesurfer_hipposubfield/post_processing"
+ref_dir="/vols/Data/psychiatry/BHC/SUBPROJECTS/BHC_hippo_seg"
+# Transform masks
+for dir in $seg_dir/HP*; do
+    cd $dir
+    echo "Checking ${dir##*/}..."
+
+       if ! [ -f "${dir##*/}_R_hippocampus_ToBrain_binarised.nii.gz" ]; then
+
+
+          input_left_img="lh_hipp.nii.gz"
+          input_right_img="rh_hipp.nii.gz"
+          ref_img=$ref_dir/${dir##*/}/${dir##*/}_T1_brain.nii.gz
+
+          # Apply FLIRT with rigid body transformations to map them on ground truth image
+          flirt -in $input_left_img -ref $ref_img -applyxfm -usesqform -out T1_orig_L_hippocampus_ToBrain.nii.gz
+          flirt -in $input_right_img -ref $ref_img -applyxfm -usesqform -out T1_orig_R_hippocampus_ToBrain.nii.gz
+
+          # Binarize them to create masks for further comparison
+          fslmaths T1_orig_L_hippocampus_ToBrain.nii.gz -thr 0.5 -bin T1_orig_L_hippocampus_ToBrain_binarised.nii.gz
+          fslmaths T1_orig_R_hippocampus_ToBrain.nii.gz -thr 0.5 -bin T1_orig_R_hippocampus_ToBrain_binarised.nii.gz
+
+          echo "${dir##*/}: Finished"
+       else
+          echo "${dir##*/}: outputs already exist..proceeding to next step"
+       fi
+done

freesurfer_hipposubfields_error_map.sh

+###### START ###############
+
+# Denote path to manual labels and auto labels, and an output path
+pathManual=$1
+pathAuto=$2
+subj=$3
+pathT1=$pathAuto
+##### Calculate_FN_FP ########
+# Input variables
+hemisphere=(L R)
+error=(FN FP)
+
+
+for dir in $pathAuto/$subj; do
+
+    
+    for h in "${hemisphere[@]}"; do
+
+        inputManual="${pathManual}/${dir##*/}/${dir##*/}_${h}hpc_mask.nii.gz"
+        inputAuto="${pathAuto}/${dir##*/}/T1_orig_${h}_hippocampus_ToBrain_binarised.nii.gz" #change file naming convention per method
+        
+        
+        # Check if automatic segmentation file exists
+        if [ -f "$inputAuto" ]; then
+            # Calculate false negatives and false positives
+            fslmaths "$inputManual" -sub "$inputAuto" -bin "${pathAuto}/${dir##*/}/${dir##*/}_${h}_FN.nii.gz"
+            fslmaths "$inputAuto" -sub "$inputManual" -bin "${pathAuto}/${dir##*/}/${dir##*/}_${h}_FP.nii.gz"
+        else
+            echo "Error: $inputAuto doesn't exist, skipping it"
+        fi
+    done
+done
+
+###### BET ###########
+# Brain extract the original T1 for use in FLIRT
+#for dir in "$pathT1"/$subj; do
+#    bet $pathT1/${dir##*/}/tool2raw.nii.gz $pathT1/${dir##*/}/${dir##*/}_brain.nii.gz -f 0.5 -g 0
+#done
+
+##### BET is not needed since ground truth images are already brain extracted and hsf_map_segs_groundtruth has aligned T1_orig images to brain extracted space 
+
+
+###### FLIRT ########
+# Register T1 to MNI 
+for dir in "$pathT1"/$subj; do
+
+        flirt -in "$pathManual/${dir##*/}/${dir##*/}_T1_brain.nii.gz" -ref "$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz" -dof 12 -out "$pathT1/${dir##*/}/${dir##*/}_toMNIlin" -omat "$pathT1/${dir##*/}/${dir##*/}_toMNIlin.mat"
+        echo "Done: ${dir##*/}"
+
+done
+
+
+######## FNIRT ###########
+# Transform T1 into MNI space using FNIRT
+for dir in "$pathT1"/$subj; do
+
+        fnirt --in=$pathT1/${dir##*/}/T1_orig_ToBrain.nii.gz --aff="$pathT1/${dir##*/}/${dir##*/}_toMNIlin.mat" --config=$FSLDIR/etc/flirtsch/T1_2_MNI152_2mm.cnf --iout="$pathT1/${dir##*/}/${dir##*/}_toMNInonlin" --cout="$pathT1/${dir##*/}/${dir##*/}_toMNI_coef" --fout="$pathT1/${dir##*/}/${dir##*/}_toMNI_warp"
+        echo "Done: ${dir##*/}"
+
+done
+
+######### Warp_FN_FP_to_MNI #############
+# Paths
+
+# Variables
+
+# Use warps from FNIRT to transform FN and FP maps into MNI space
+for dir in "$pathT1"/$subj; do
+
+    for h in "${hemisphere[@]}"; do
+
+        for err in "${error[@]}"; do
+
+            applywarp -i "${pathAuto}/${dir##*/}/${dir##*/}_${h}_${err}.nii.gz" -r "$FSLDIR/data/standard/MNI152_T1_1mm" -w "$pathT1/${dir##*/}/${dir##*/}_toMNI_warp.nii.gz" -o "$pathT1/${dir##*/}/${subj}_${h}_${err}_MNI.nii.gz"
+        
+        done
+    done
+    echo "Done: ${dir##*/}"
+done