From d643809ba7602ba3524b7dd4c091537a8b77c8ff Mon Sep 17 00:00:00 2001 From: Sebastien Tourbier Date: Fri, 10 May 2019 14:41:20 +0200 Subject: [PATCH] FIX: filename typos + extra line in list of scans --- data/code/create_scan_preproc_json.sh | 2 +- data/code/sub-01_ses-01_scans.txt | 1 - data/code/sub-01_ses-02_scans.txt | 1 - data/code/superresolution_pipeline.sh | 7 +++++-- .../anat/sub-01_run-1_desc-brain_mask.nii.gz | Bin 12779 -> 0 bytes .../anat/sub-01_run-2_desc-brain_mask.nii.gz | Bin 12979 -> 0 bytes .../anat/sub-01_run-3_desc-brain_mask.nii.gz | Bin 12752 -> 0 bytes .../anat/sub-01_run-4_desc-brain_mask.nii.gz | Bin 12773 -> 0 bytes .../anat/sub-01_run-5_desc-brain_mask.nii.gz | Bin 12834 -> 0 bytes .../anat/sub-01_run-6_desc-brain_mask.nii.gz | Bin 12857 -> 0 bytes 10 files changed, 6 insertions(+), 5 deletions(-) delete mode 100755 data/derivatives/manual_masks/sub-01/anat/sub-01_run-1_desc-brain_mask.nii.gz delete mode 100755 data/derivatives/manual_masks/sub-01/anat/sub-01_run-2_desc-brain_mask.nii.gz delete mode 100755 data/derivatives/manual_masks/sub-01/anat/sub-01_run-3_desc-brain_mask.nii.gz delete mode 100755 data/derivatives/manual_masks/sub-01/anat/sub-01_run-4_desc-brain_mask.nii.gz delete mode 100755 data/derivatives/manual_masks/sub-01/anat/sub-01_run-5_desc-brain_mask.nii.gz delete mode 100755 data/derivatives/manual_masks/sub-01/anat/sub-01_run-6_desc-brain_mask.nii.gz diff --git a/data/code/create_scan_preproc_json.sh b/data/code/create_scan_preproc_json.sh index e1dd92e94..4b5585e4b 100644 --- a/data/code/create_scan_preproc_json.sh +++ b/data/code/create_scan_preproc_json.sh @@ -22,4 +22,4 @@ cat < $OUTPUT_JSON \ No newline at end of file +) > $OUTPUT_JSON diff --git a/data/code/sub-01_ses-01_scans.txt b/data/code/sub-01_ses-01_scans.txt index 24aa5763f..bdd0175d3 100644 --- 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 index 18cd1827d..d79fd3ad0 100644 --- 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 index e83f9316a..5c9f619b1 100755 --- 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 deleted file mode 100755 index 9e7945a8ae9d7658453c30648c2219a0f49465fa..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12779 zcmeHMYgAKb7EKHz3|$(hLua*ie66l_D2igSO_gVvj?<>{FcWE&TA~%5RE@0|SrlVn zO|fg#+BH_t%DYY^M5$U4I*Di;r**Z8uYj$l7wEJV1&I%YC?RCd{&ETN)g}F5*Vypu 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