Minimally update batch_single_subject.sh to produce the same metric CSVs as batch_processing.sh#35
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This commands should produce the necessary files to run `test_batch_processing.yml`, albeit likely with different results.
The previous commit added commands to `batch_single_subject.sh` to reproduce the existing `batch_processing.sh` metrics EXACTLY. But, to do so, many outdated commands and methods were needed. This commit removes the outdated methods, and tries to reproduce the relevant metric files using only the commands that were already present within `batch_single_subject.sh`. Doing this will fundamentally change the values we produced (due to different underlying methods), but it allows us to keep the pipeline we've already developed for the SCT Course over the years. Only minimal changes to the existing commands were necessary, and the changes should be painless to port over to the SCT Course. This provides a smooth transition from having 2 scripts (batch_processing.sh and batch_single_subject.sh) to just 1 script (batch_single_subject.sh), allowing us to get rid of the old script entirely. For documentation on what exactly changed here from old -> new, refer to the extensive comments in the previous commit.
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I am working on this now. It looks like there are more deviations between the tutorials and the Diff between tutorials and script(venv_sct) joshua@jn/3508-merge-example-datasets-and-batch-scripts >
$ [~/repos/spinalcordtoolbox] # cd /home/joshua/repos/spinalcordtoolbox
python3 testing/batch_single_subject/extract_commands.py \
--compare \
--script-path ~/repos/sct_tutorial_data/single_subject/batch_single_subject.sh
INFO: Found 113 RST tutorial files in /home/joshua/repos/spinalcordtoolbox/documentation/source/user_section/tutorials
INFO: Found 93 unique invocations in tutorials
INFO: Reading script from /home/joshua/repos/sct_tutorial_data/single_subject/batch_single_subject.sh
INFO: Found 82 unique invocations in scriptLegend: ' ' = same, '-' = tutorials only, '+' = script only
sct_analyze_lesion -m t2_lesion_seg.nii.gz -s t2_sc_seg.nii.gz -f label -qc ~/qc_singleSubj
sct_analyze_lesion -m t2_lesion_seg.nii.gz -s t2_sc_seg.nii.gz -qc ~/qc_singleSubj
- sct_compute_ascor -i-SC t2_compressed_seg.nii.gz -i-canal t2_compressed_canal_seg.nii.gz -perlevel 1 -o ascor.csv
+ sct_compute_ascor -i-SC t2_seg.nii.gz -i-canal t2_canal_seg.nii.gz -perlevel 1 -o ascor.csv
sct_compute_compression -i t2_compressed_seg.nii.gz -vertfile t2_compressed_seg_labeled.nii.gz -l t2_compressed_labels-compression.nii.gz -metric diameter_AP -normalize-hc 0 -o ap_ratio.csv
sct_compute_compression -i t2_compressed_seg.nii.gz -vertfile t2_compressed_seg_labeled.nii.gz -l t2_compressed_labels-compression.nii.gz -metric diameter_AP -normalize-hc 1 -o ap_ratio_norm_PAM50.csv
sct_compute_mtr -mt0 mt0_reg.nii.gz -mt1 mt1.nii.gz
sct_create_mask -i dmri_dwi_mean.nii.gz -p centerline,dmri_dwi_mean_seg.nii.gz -size 35mm
- sct_create_mask -i fmri.nii.gz -p centerline,t2_seg_reg.nii.gz -size 35mm
+ sct_create_mask -i fmri.nii.gz -p centerline,t2_seg_reg.nii.gz -size 35mm -f cylinder
+ sct_create_mask -i mt1.nii.gz -p centerline,mt1_seg.nii.gz -size 35mm -f cylinder -o mask_mt1.nii.gz
- sct_create_mask -i mt1.nii.gz -p centerline,mt1_seg.nii.gz -size 35mm -o mask_mt1.nii.gz
- sct_create_mask -i t1.nii.gz -p centerline,t1_seg.nii.gz -size 35mm -o mask_t1.nii.gz
- sct_create_mask -i t2.nii.gz -p centerline,t2_seg.nii.gz -size 35mm -o mask_t2.nii.gz
- sct_crop_image -i IMAGE_UNIT1 -m IMAGE_seg -dilate 30x30x5
+ sct_crop_image -i fmri_moco_mean.nii.gz -m mask_fmri.nii.gz -b 0
- sct_crop_image -i t1.nii.gz -m mask_t1.nii.gz
- sct_crop_image -i t2.nii.gz -m mask_t2.nii.gz
sct_deepseg -h
sct_deepseg graymatter -i t2s.nii.gz -o t2s_gmseg.nii.gz -qc ~/qc_singleSubj
- sct_deepseg lesion_ms -i t2.nii.gz -qc ~/qc_singleSubj
+ sct_deepseg lesion_ms -i t2.nii.gz -qc ~/qc_singleSubj -qc-seg t2_seg.nii.gz -single-fold
- sct_deepseg lesion_ms_mp2rage -i IMAGE_UNIT1 -qc ~/qc_singleSubj
sct_deepseg lesion_sci_t2 -i t2.nii.gz -qc ~/qc_singleSubj
- sct_deepseg rootlets -i t2.nii.gz -o t2_rootlets.nii.gz -qc ~/qc_singleSubj
+ sct_deepseg rootlets -i t2.nii.gz -qc ~/qc_singleSubj
+ sct_deepseg sc_canal_t2 -i t2.nii.gz -qc ~/qc_singleSubj
- sct_deepseg sc_canal_t2 -i t2_compressed.nii.gz -o t2_compressed_canal_seg.nii.gz -qc ~/qc_singleSubj
+ sct_deepseg sc_epi -i fmri_moco_mean_crop.nii.gz -qc ~/qc_singleSubj
sct_deepseg sc_lumbar_t2 -i t2_lumbar.nii.gz -qc ~/qc_singleSubj
- sct_deepseg sc_lumbar_t2 -install
- sct_deepseg spinalcord -i IMAGE_UNIT1 -o IMAGE_seg
sct_deepseg spinalcord -i dmri_dwi_mean.nii.gz -qc ~/qc_singleSubj
sct_deepseg spinalcord -i dmri_moco_dwi_mean.nii.gz -qc ~/qc_singleSubj
sct_deepseg spinalcord -i fmri_moco_mean.nii.gz -qc ~/qc_singleSubj/
sct_deepseg spinalcord -i mt1.nii.gz -qc ~/qc_singleSubj
- sct_deepseg spinalcord -i t1.nii.gz -qc ~/qc_singleSubj
+ sct_deepseg spinalcord -i t1.nii.gz -qc ~/qc_singleSubj/
sct_deepseg spinalcord -i t1_smooth.nii.gz -qc ~/qc_singleSubj
- sct_deepseg spinalcord -i t2.nii.gz
+ sct_deepseg spinalcord -i t2.nii.gz -o test/t2_seg_2.nii.gz
sct_deepseg spinalcord -i t2.nii.gz -qc ~/qc_singleSubj
sct_deepseg spinalcord -i t2_compressed.nii.gz -qc ~/qc_singleSubj
sct_deepseg spinalcord -i t2s.nii.gz -qc ~/qc_singleSubj
sct_deepseg spine -i t2.nii.gz -label-vert 1 -qc ~/qc_singleSubj
sct_deepseg spine -i t2.nii.gz -qc ~/qc_singleSubj
- sct_deepseg_lesion -i t2.nii.gz -c t2
sct_detect_pmj -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
sct_dmri_compute_dti -i dmri_moco.nii.gz -bval bvals.txt -bvec bvecs.txt
sct_dmri_moco -i dmri.nii.gz -m mask_dmri_dwi_mean.nii.gz -bvec bvecs.txt -qc ~/qc_singleSubj -qc-seg dmri_dwi_mean_seg.nii.gz
sct_dmri_separate_b0_and_dwi -i dmri.nii.gz -bvec bvecs.txt
- sct_download_data -d PAM50
- sct_download_data -d manual-correction -o manual-correction
+ sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 4,5 -method wa -z 2:14 -o fa_in_cst.csv
sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 51 -method map -vert 2:5 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 -o fa_in_wm.csv
sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 4,5 -z 5:15 -o mtr_in_cst.csv
- sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 51 -o mtr_in_wm.csv
+ sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 51 -vert 2:5 -o mtr_in_wm.csv
sct_extract_metric -i mtr.nii.gz -f label/atlas -method map -l 53 -vert 2:4 -vertfile label/template/PAM50_levels.nii.gz -o mtr_in_dc.csv
sct_extract_metric -i t2s.nii.gz -f t2s_gmseg.nii.gz -method bin -z 2:12 -o t2s_value.csv -append 1
sct_extract_metric -i t2s.nii.gz -f t2s_wmseg.nii.gz -method bin -z 2:12 -o t2s_value.csv
sct_flatten_sagittal -i t1.nii.gz -s t1_seg.nii.gz
sct_fmri_compute_tsnr -i fmri.nii.gz
sct_fmri_compute_tsnr -i fmri_moco.nii.gz
sct_fmri_moco -i fmri.nii.gz -m mask_fmri.nii.gz -qc ~/qc_singleSubj -qc-seg t2_seg_reg.nii.gz
- sct_label_utils -i mt1_seg.nii.gz -create-seg-mid 4 -o label_c3c4.nii.gz
- sct_label_utils -i t2.nii.gz -create-viewer 3 -o label_c2c3.nii.gz -msg "Click at the posterior tip of C2/C3 inter-vertebral disc"
- sct_label_utils -i t2.nii.gz -create-viewer 3,4,5 -o labels_disc.nii.gz -msg "Place labels at the posterior tip of each inter-vertebral disc. E.g. Label 3: C2/C3, Label 4: C3/C4, etc."
+ sct_label_utils -i t2_compressed.nii.gz -create 30,152,99,1.0:30,156,118,1.0:30,157,140,1.0:31,160,159,1.0 -o t2_compressed_labels-compression.nii.gz
sct_label_utils -i t2_lumbar.nii.gz -create 27,76,187,17:27,79,80,60 -o t2_lumbar_labels.nii.gz -qc ~/qc_singleSubj
- sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 3,9 -o t2_labels_vert.nii.gz
sct_label_utils -i t2_totalspineseg_discs.nii.gz -keep 3,9 -o t2_labels_vert.nii.gz
+ sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -discfile t2_totalspineseg_discs.nii.gz
- sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -initlabel label_c2c3.nii.gz -qc ~/qc_singleSubj
- sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc ~/qc_singleSubj
sct_label_vertebrae -i t2_compressed.nii.gz -s t2_compressed_seg.nii.gz -c t2 -qc ~/qc_singleSubj
sct_maths -i fmri.nii.gz -mean t -o fmri_mean.nii.gz
sct_maths -i t2s_seg.nii.gz -sub t2s_gmseg.nii.gz -thr 0 -o t2s_wmseg.nii.gz
+ sct_process_segmentation -i t2_seg.nii.gz -anat t2.nii.gz -vert 2:3 -discfile t2_totalspineseg_discs.nii.gz -perlevel 1 -o csa_perlevel.csv
- sct_process_segmentation -i t2_seg.nii.gz -anat t2.nii.gz -vert 3:4 -discfile t2_totalspineseg_discs.nii.gz -perlevel 1 -o csa_perlevel.csv
- sct_process_segmentation -i t2_seg.nii.gz -discfile t2_totalspineseg_discs.nii.gz -perslice 1 -normalize-PAM50 1 -o csa_PAM50.csv
+ sct_process_segmentation -i t2_seg.nii.gz -discfile t2_totalspineseg_discs.nii.gz -perslice 1 -normalize-PAM50 1 -o csa_pam50.csv
+ sct_process_segmentation -i t2_seg.nii.gz -pmj t2_pmj.nii.gz -pmj-distance 60 -pmj-extent 30 -o csa_pmj.csv -qc ~/qc_singleSubj -qc-image t2.nii.gz
- sct_process_segmentation -i t2_seg.nii.gz -pmj t2_pmj.nii.gz -pmj-distance 64 -pmj-extent 30 -o csa_pmj.csv -qc ~/qc_singleSubj -qc-image t2.nii.gz
+ sct_process_segmentation -i t2_seg.nii.gz -vert 2:3 -discfile t2_totalspineseg_discs.nii.gz -o csa_c2c3.csv
- sct_process_segmentation -i t2_seg.nii.gz -vert 3:4 -discfile t2_totalspineseg_discs.nii.gz -o csa_c3c4.csv
sct_process_segmentation -i t2_seg.nii.gz -z 30:35 -discfile t2_totalspineseg_discs.nii.gz -perslice 1 -o csa_perslice.csv
- sct_process_segmentation -i t2s_gmseg.nii.gz -o csa_gm.csv -perslice 1 -angle-corr 0
+ sct_process_segmentation -i t2s_gmseg.nii.gz -o csa_gm_perslice.csv -perslice 1 -angle-corr 0
+ sct_process_segmentation -i t2s_gmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_gm.csv -centerline t2s_seg.nii.gz -centerline-exclude-missing 1
- sct_process_segmentation -i t2s_wmseg.nii.gz -o csa_wm.csv -perslice 1 -angle-corr 0
+ sct_process_segmentation -i t2s_wmseg.nii.gz -o csa_wm_perslice.csv -perslice 1 -angle-corr 0
+ sct_process_segmentation -i t2s_wmseg.nii.gz -vert 2:5 -perlevel 1 -o csa_wm.csv -centerline t2s_seg.nii.gz -centerline-exclude-missing 1
sct_qc -i fmri_tsnr.nii.gz -d fmri_moco_tsnr.nii.gz -s fmri_moco_mean_seg.nii.gz -p sct_fmri_compute_tsnr -qc ~/qc_singleSubj/
+ sct_qc -i t2.nii.gz -s t2_labels_vert.nii.gz -p sct_label_utils -qc ~/qc_singleSubj
sct_qc -i t2_lumbar.nii.gz -s t2_lumbar_labels.nii.gz -p sct_label_utils -qc ~/qc_singleSubj
+ sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t1.nii.gz -iseg "${SCT_DIR}"/data/PAM50/template/PAM50_cord.nii.gz -d dmri_moco_dwi_mean.nii.gz -dseg dmri_moco_dwi_mean_seg.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -qc ~/qc_singleSubj
+ sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t2.nii.gz -iseg "${SCT_DIR}"/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -m mask_mt1.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -owarp warp_template2mt.nii.gz -qc ~/qc_singleSubj
+ sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t2.nii.gz -iseg "${SCT_DIR}"/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz -owarp warp_template2mt.nii.gz -qc ~/qc_singleSubj
+ sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t2s.nii.gz -iseg "${SCT_DIR}"/data/PAM50/template/PAM50_cord.nii.gz -d fmri_moco_mean.nii.gz -dseg fmri_moco_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,algo=syn,metric=CC,iter=3,slicewise=1 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2fmri.nii.gz -owarpinv warp_fmri2template.nii.gz -qc ~/qc_singleSubj
+ sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t2s.nii.gz -iseg "${SCT_DIR}"/data/PAM50/template/PAM50_wm.nii.gz -d t2s.nii.gz -dseg t2s_wmseg.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz -param step=1,type=seg,algo=rigid:step=2,type=seg,metric=CC,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,metric=CC,algo=syn,slicewise=1,iter=2 -qc ~/qc_singleSubj
- sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t1.nii.gz" -iseg "${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz" -d dmri_moco_dwi_mean.nii.gz -dseg dmri_moco_dwi_mean_seg.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -qc ~/qc_singleSubj
- sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t2.nii.gz" -iseg "${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz" -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz -owarp warp_template2mt.nii.gz -qc ~/qc_singleSubj
- sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t2s.nii.gz" -d fmri_moco_mean.nii.gz -dseg t2_seg_reg.nii.gz -param step=1,type=im,algo=syn,metric=CC,iter=5,slicewise=0 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2fmri.nii.gz -owarpinv warp_fmri2template.nii.gz -qc ~/qc_singleSubj
- sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t2s.nii.gz" -iseg "${SCT_DIR}/data/PAM50/template/PAM50_wm.nii.gz" -d t2s.nii.gz -dseg t2s_wmseg.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz -param step=1,type=seg,algo=rigid:step=2,type=seg,metric=CC,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,metric=CC,algo=syn,slicewise=1,iter=2 -qc ~/qc_singleSubj
- sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -m mask_mt1.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -owarp warp_template2mt.nii.gz -qc ~/qc_singleSubj
sct_register_multimodal -i ../t2/t2_seg.nii.gz -d fmri_mean.nii.gz -identity 1
sct_register_multimodal -i mt0.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -m mask_mt1.nii.gz -param step=1,type=im,algo=slicereg,metric=CC -x spline -qc ~/qc_singleSubj
- sct_register_multimodal -i t1_crop.nii.gz -d ../t2/t2_crop.nii.gz -param step=1,type=im,algo=dl -qc ~/qc_singleSubj -dseg ../t2/t2_seg.nii.gz
- sct_register_to_template -i mt1.nii.gz -s mt1_seg.nii.gz -ldisc label_c3c4.nii.gz -ref subject -param step=1,type=seg,algo=centermassrot:step=2,type=seg,algo=bsplinesyn,slicewise=1
sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_labels_vert.nii.gz -c t2 -qc ~/qc_singleSubj
+ sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_labels_vert.nii.gz -qc ~/qc_singleSubj -ofolder advanced_param -c t2 -param step=1,type=seg,algo=rigid:step=2,type=seg,metric=CC,algo=bsplinesyn,slicewise=1,iter=3:step=3,type=im,metric=CC,algo=syn,slicewise=1,iter=2
- sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -lrootlet t2_rootlets.nii.gz -c t2 -ofolder rootlets-reg -qc ~/qc_singleSubj
sct_register_to_template -i t2_lumbar.nii.gz -s t2_lumbar_seg.nii.gz -ldisc t2_lumbar_labels.nii.gz -c t2 -qc ~/qc_singleSubj -param step=1,type=seg,algo=centermassrot:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,iter=3,slicewise=0:step=3,type=im,algo=syn,metric=CC,iter=3,slicewise=0
- sct_run_batch -script process_data.sh -config config.yml
- sct_run_batch -script process_data.sh -path-data data/ -path-output output_correction -jobs 3
sct_smooth_spinalcord -i t1.nii.gz -s t1_seg.nii.gz
sct_warp_template -d dmri_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc ~/qc_singleSubj
sct_warp_template -d fmri_moco_mean.nii.gz -w warp_template2fmri.nii.gz -a 0 -qc ~/qc_singleSubj
sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -a 1 -qc ~/qc_singleSubj
+ sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -qc ~/qc_singleSubj
sct_warp_template -d t2.nii.gz -w ../t2/warp_template2anat.nii.gz
sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0 -qc ~/qc_singleSubj
+ sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz -qc ~/qc_singleSubj |
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Description
This PR updates the
batch_single_subject.shscript so that it produces the same CSV files thatbatch_processing.shproduces.Here is what the old
batch_processing.shscript tested:t2/csa_c2c3.csv-0-MEAN(area)t2/csa_pmj.csv-0-MEAN(area)t2/csa_pam50.csv-38-MEAN(area)t2s/csa_gm.csv-3-MEAN(area)t2s/csa_wm.csv-3-MEAN(area)mt/mtr_in_wm.csv-0-MAP()dmri/fa_in_cst.csv-0-WA()dmri/fa_in_cst.csv-1-WA()These files are now generated by this repo, instead.
Disclaimer
Even though the output files are now the same, the underlying SCT commands are different between
batch_processing.shandbatch_single_subject.sh. For an overview of all of the differences, please read the comments present in this commit: db7730aI used that commit to isolate the old
batch_processing.shcommands, and tested them with SCT to make sure the test passed:batch_processing.shwithbatch_single_subject.shspinalcordtoolbox#5185Then, I replaced the old commands with our "modern" commands in the commit 9e43050. This will fundamentally change the segmentation/registration methods, and means that the new values aren't really comparable to the old ones. But, it does at least preserve the entire testing infrastructure we built previously (i.e.
batch_single_subject.shis now a "drop-in replacement" forbatch_processing.sh).Next steps
batch_processing.shtests.batch_single_subject.shin tandem.)