FIX: filename typos + extra line in list of scans

Medical-Image-Analysis-Laboratory · May 10, 2019 · d643809 · d643809
1 parent b520fc3
commit d643809
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Showing 10 changed files with 6 additions and 5 deletions.
diff --git a/data/code/create_scan_preproc_json.sh b/data/code/create_scan_preproc_json.sh
@@ -22,4 +22,4 @@ cat <<EOF
 }
 
 EOF
-) > $OUTPUT_JSON
+) > $OUTPUT_JSON
diff --git a/data/code/sub-01_ses-01_scans.txt b/data/code/sub-01_ses-01_scans.txt
@@ -1,4 +1,3 @@
 sub-01_run-1_T2w axial
 sub-01_run-2_T2w coronal
 sub-01_run-3_T2w sagittal
-
diff --git a/data/code/sub-01_ses-02_scans.txt b/data/code/sub-01_ses-02_scans.txt
@@ -4,4 +4,3 @@ sub-01_run-3_T2w sagittal
 sub-01_run-4_T2w coronal
 sub-01_run-5_T2w sagittal
 sub-01_run-6_T2w sagittal
-
diff --git a/data/code/superresolution_pipeline.sh b/data/code/superresolution_pipeline.sh
@@ -122,8 +122,11 @@ do
 			echo "Process stack $stack with $orientation orientation..."
 
 		    #Reorient the image
-			mialsrtkOrientImage -i ${PATIENT_DIR}/${stack}.nii.gz -o $RESULTS/${stack}_reo_iteration_${ITER}.nii.gz -O "$orientation"
-			mialsrtkOrientImage -i ${PATIENT_MASK_DIR}/${stack}_desc-brain_mask.nii.gz -o $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz -O "$orientation"
+			#mialsrtkOrientImage -i ${PATIENT_DIR}/${stack}.nii.gz -o $RESULTS/${stack}_reo_iteration_${ITER}.nii.gz -O "$orientation"
+			#mialsrtkOrientImage -i ${PATIENT_MASK_DIR}/${stack}_desc-brain_mask.nii.gz -o $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz -O "$orientation"
+
+			cp "${PATIENT_DIR}/${stack}.nii.gz" "$RESULTS/${stack}_reo_iteration_${ITER}.nii.gz"
+			cp "${PATIENT_MASK_DIR}/${stack}_desc-brain_mask.nii.gz" "$RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz"
 
 			#denoising on reoriented images
 			weight="0.1"

diff --git a/data/derivatives/manual_masks/sub-01/anat/sub-01_run-1_desc-brain_mask.nii.gz b/data/derivatives/manual_masks/sub-01/anat/sub-01_run-1_desc-brain_mask.nii.gz
diff --git a/data/derivatives/manual_masks/sub-01/anat/sub-01_run-2_desc-brain_mask.nii.gz b/data/derivatives/manual_masks/sub-01/anat/sub-01_run-2_desc-brain_mask.nii.gz
diff --git a/data/derivatives/manual_masks/sub-01/anat/sub-01_run-3_desc-brain_mask.nii.gz b/data/derivatives/manual_masks/sub-01/anat/sub-01_run-3_desc-brain_mask.nii.gz
diff --git a/data/derivatives/manual_masks/sub-01/anat/sub-01_run-4_desc-brain_mask.nii.gz b/data/derivatives/manual_masks/sub-01/anat/sub-01_run-4_desc-brain_mask.nii.gz
diff --git a/data/derivatives/manual_masks/sub-01/anat/sub-01_run-5_desc-brain_mask.nii.gz b/data/derivatives/manual_masks/sub-01/anat/sub-01_run-5_desc-brain_mask.nii.gz
diff --git a/data/derivatives/manual_masks/sub-01/anat/sub-01_run-6_desc-brain_mask.nii.gz b/data/derivatives/manual_masks/sub-01/anat/sub-01_run-6_desc-brain_mask.nii.gz
-Original file line number
+Diff line change
@@ Expand Up / @@ -22,4 +22,4 @@ cat <<EOF @@
     }
     EOF
-    ) > $OUTPUT_JSON
+    ) > $OUTPUT_JSON
Original file line number	Diff line number	Diff line change
Expand Up		@@ -4,4 +4,3 @@ sub-01_run-3_T2w sagittal
		sub-01_run-4_T2w coronal
		sub-01_run-5_T2w sagittal
		sub-01_run-6_T2w sagittal