Grey matter segmentation CSV: Vert Level Missing

ambaf · October 29, 2020, 3:04pm

Here is the second half:


Move warping fields...
cp step2Warp.nii.gz /tmp/sct-20201029153546.541065-register-ocgl30mg
cp step2InverseWarp.nii.gz /tmp/sct-20201029153546.541065-register-ocgl30mg
rm -rf /tmp/sct-20201029154556.837548-register-tzn1pfg9

Concatenate transformations...

Parse list of warping fields...

Check file existence...
  OK: dest.nii
  OK: /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/analysisFiles/warp_template2anat.nii.gz
  OK: warp_forward_1.mat
  OK: warp_forward_2.nii.gz
/home/nirims/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.mat /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/analysisFiles/warp_template2anat.nii.gz # in /tmp/sct-20201029153546.541065-register-ocgl30mg

Generate output files...
  File created: warp_src2dest.nii.gz

Parse list of warping fields...

Check file existence...
  OK: src.nii
  OK: warp_inverse_2.nii.gz
  OK: warp_forward_1.mat
  OK: /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/analysisFiles/warp_anat2template.nii.gz
/home/nirims/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R src.nii /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/analysisFiles/warp_anat2template.nii.gz -i warp_forward_1.mat warp_inverse_2.nii.gz # in /tmp/sct-20201029153546.541065-register-ocgl30mg

Generate output files...
  File created: warp_dest2src.nii.gz

Apply transfo source --> dest...

Parse list of warping fields...

Get dimensions of data...
  141 x 141 x 991 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20201029153546.541065-register-ocgl30mg
Copy affine matrix from destination space to make sure qform/sform are the same.

Done! To view results, type:
fsleyes dest.nii src_reg.nii &


Apply transfo dest --> source...

Parse list of warping fields...

Get dimensions of data...
  512 x 448 x 26 x 1

Apply transformation...

Apply transformation and resample to destination space...
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20201029153546.541065-register-ocgl30mg
Copy affine matrix from destination space to make sure qform/sform are the same.

Done! To view results, type:
fsleyes src.nii dest_reg.nii &


Generate output files...
  File created: PAM50_t2s_reg.nii.gz
  File created: 2020subj1_reg.nii
  File created: warp_PAM50_t2s22020subj1.nii.gz
  File created: warp_2020subj12PAM50_t2s.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20201029153546.541065-register-ocgl30mg

Finished! Elapsed time: 966s

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
Mask type float64
Successfully generated the QC results in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/csvOutcome/anonData/qc/_json/qc_2020_10_29_155158.590531.json
Use the following command to see the results in a browser:
xdg-open "/media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/csvOutcome/anonData/qc/index.html"

Done! To view results, type:
fsleyes /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2s.nii.gz 2020subj1_reg.nii &


Done! To view results, type:
fsleyes 2020subj1.nii PAM50_t2s_reg.nii.gz &

mv: Aufruf von stat für 'warp_t2s2PAM50_2020subj1.nii.gz' nicht möglich: Datei oder Verzeichnis nicht gefunden

--
Spinal Cord Toolbox (4.3)

Folder ../../csvOutcome/anonData/qc has been created.

Check parameters:
  Working directory ........ /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
  Destination image ........ 2020subj1.nii
  Warping field ............ warp_template2t2s.nii.gz
  Path template ............ /home/nirims/sct_4.3/data/PAM50
  Output folder ............ label


WARP TEMPLATE:
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_t1.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_t1.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_t2.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_t2s.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_cord.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_cord.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_wm.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_wm.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_gm.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_gm.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_csf.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_csf.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_levels.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_levels.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_levels_continuous.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_body.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_label_body.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_disc.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_label_disc.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_discPosterior.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_spine.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_spine.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_centerline.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_centerline.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -n NearestNeighbor # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
cp /home/nirims/sct_4.3/data/PAM50/template/info_label.txt label/template

WARP ATLAS OF WHITE MATTER TRACTS:
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_00.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_01.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_02.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_03.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_04.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_05.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_06.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_07.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_08.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_09.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_10.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_11.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_12.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_13.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_14.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_15.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_16.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_17.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_18.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_19.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_20.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_21.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_22.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_23.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_24.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_25.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_26.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_27.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_28.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_29.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_30.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_31.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_32.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_33.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_34.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_35.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
/home/nirims/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /home/nirims/sct_4.3/data/PAM50/atlas/PAM50_atlas_36.nii.gz -r 2020subj1.nii -t warp_template2t2s.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -n Linear # in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/anonData/subj1
cp /home/nirims/sct_4.3/data/PAM50/atlas/info_label.txt label/atlas

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
Successfully generated the QC results in /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/csvOutcome/anonData/qc/_json/qc_2020_10_29_155605.785358.json
Use the following command to see the results in a browser:
xdg-open "/media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/csvOutcome/anonData/qc/index.html"

Done! To view results, type:
fsleyes 2020subj1.nii -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm red-yellow -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 &


--
Spinal Cord Toolbox (4.3)

Compute shape analysis: 100%|#################| 26/26 [00:00<00:00, 47.05iter/s]

Done! To view results, type:
xdg-open /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/csvOutcome/anonData/subj1/2020subj1_gm_CSA.csv


--
Spinal Cord Toolbox (4.3)

Compute shape analysis: 100%|#################| 26/26 [00:00<00:00, 28.76iter/s]

Done! To view results, type:
xdg-open /media/sf_GemeinsamerOrdner/SCT/Testdaten/miniTrialGMWM/csvOutcome/anonData/subj1/2020subj1_wm_CSA.csv

Execution time was 1476 seconds.

ambaf · October 29, 2020, 3:05pm

And attached is a sample CSV Output.

gmCSV.xlsx (14.6 KB)

anon33887296 · October 29, 2020, 4:17pm

Thanks. Would it be possible to see what is in gm_wm_script.sh too?

anon33887296 · October 29, 2020, 5:02pm

I believe you need to pass -vert to sct_extract_metric to ask it for this output. For easier consumption by other tools, the VertLevel column was made permanent in https://github.com/neuropoly/spinalcordtoolbox/pull/2199, but you still need to enable it to actually get the output.

Do you have an idea about how we could make this more obvious?

ambaf · October 30, 2020, 11:16am

I see! Thank you. I think it was mostly confusing because of the empty column which made it seem like an error had occurred and because you can use sct_process_segmentation to get vertebral values for t1 and t2 Scans. I also thought the Atlas base Analysis was for more specific Areas of the spinal cord. But in hindsight the notes make a lot more sense now! Thank you again

jcohenadad · November 3, 2020, 2:30am

sorry for the late reply-- yes, as you and @anon33887296 figured out, you need to specify -vert in order to have the explicit levels listed in the output CSV file.

ambaf · November 11, 2020, 10:46am

Hi again!

I tried the sct_extract_metric approach on the same file, but when I use sct_warp_template after creating a mask and registering the template to the file, only a small amount of slices are successfully registered. Therefore, I only get very few output values per vertebrae.

Here I registered the template using the GM shape, but I also tried without and got the same/worse results. I used the same commands as used in the course, changing only the files.

Also, is the size in voxels given by sct_extract_metric the same as the area values given by sct_process Segmentation, just as a different measurement?

Thank you!
Amba

jcohenadad · November 11, 2020, 3:04pm

Hi @ambaf

there is clearly something wrong with your analysis pipeline. It is difficult for me to tell what is wrong: could be the segmentation, the registration, the types of inputs, the parameters, etc.

the most efficient way for me to help would be for you to share:

the images you used to generate those results
the shell script you used to generate those results. Please use relative (not absolute) file names so the script can run as is.

ambaf · November 12, 2020, 8:32am

Hi @jcohenadad,

below are the script I used for both types of template registration and the output I got from it. I have emailed you the t2* Image. Thank you!

script.sh (1.7 KB) output.txt (71.2 KB)

jcohenadad · November 12, 2020, 5:22pm

@ambaf

your script requires those inputs:

warp_template2anat.nii.gz
warp_anat2template.nii.gz

which you did not send me (you only sent the t2s).

pls send me everything needed for me to reproduce your results.

also: there is possibly something wrong with warp_template2anat.nii.gz, so it might be more efficient if you send me the sources that generated this warping field (and also include the full script to get to this)

ambaf · November 13, 2020, 12:30pm

Hi @jcohenadad,

To be sure I wasn’t making a mistake, I rewrote the cript only copy-pasting from the Course script. I’ve attached what I used. With this script get:

I believe my first error was due to my using the wrong warp_template2anat and warp_anat2template files, but now using the correct ones I still only get data for half the slices. I have sent you the t2 file I used and the warp_template2anat file it created. However, the warp_anat2template file is too large to send.

Thank you!
Amba
scriptUsed.sh (1.2 KB)

jcohenadad · November 13, 2020, 1:37pm

@ambaf The problem is caused by the T2 and T2* images not being in the same physical coordinate system, as shown in the image below:

This is likely due to the two images being acquired with patient repositioning in between.

If you absolutely need to process these data, then you need to manually set the vertebral level on the T2*. We kind of see the intervertebral discs, so you could assign the slice number and use it before sct_register_to_template (with flag: -ref subject). Or, if you know how the FOV was placed (e.g., center of FOV at disc XX), you could also use that information, as exemplified in this pipeline.

ambaf · November 19, 2020, 10:02am

@jcohenadad aah, I see! Thank you. Luckily the majority of the data doesn’t have repositioning between the two scans, so in this case it should be fine after all. Thank you for spotting this!

Best wishes,
Amba

ambaf · November 20, 2020, 12:17pm

Hi @jcohenadad,

thank you for all your help so far. I am still having trouble obtaining the per-vertebrae CSA for Grey and White matter from my T2* Images by registering them to my T2 Images. I have tried following the steps from this post Sct_label_utils display , but I get vert values of “16.889” for example. I’ve also tried using the created vertfile in the sct_extract_metric command under the -vertfile flag but get no vertLevel values. I have sent you a sample T2 and T2* file more representative of the data. Do you have any suggestions on the best way to proceed?

jcohenadad · November 20, 2020, 3:53pm

Hi,

Here are the commands:

# T2 processing
# =============
# Crop T2 with FOV from T2* data (for faster processing)
sct_crop_image -i t2_subj14.nii.gz -ref t2s_subj14.nii.gz
# Resample to isotropic resolution due to poor native R-L resolution
 sct_resample -i t2_subj14_crop.nii.gz -mm 0.8x0.8x0.8 -o t2_subj14_crop_r.nii.gz
# Segment spinal cord
sct_deepseg_sc -i t2_subj14_crop_r.nii.gz -c t2 -qc qc
# Label vertebrae
sct_label_vertebrae -i t2_subj14_crop_r.nii.gz -s t2_subj14_crop_r_seg.nii.gz -c t2 -qc qc
# T2* processing
# ==============
# Segment spinal cord
sct_deepseg_sc -i t2s_subj14.nii.gz -c t2s -qc qc
# Segment gray matter
sct_deepseg_gm -i t2s_subj14.nii.gz -qc qc
# Subtract spinal cord and gray matter masks to obtain white matter mask
sct_maths -i t2s_subj14_seg.nii.gz -sub t2s_subj14_gmseg.nii.gz -o t2s_subj14_wmseg.nii.gz
# Bring T2 vertebral labeling to T2* space for vertebral-based quantifications
sct_register_multimodal -i t2_subj14_crop_r_seg_labeled.nii.gz -d t2s_subj14.nii.gz -identity 1 -x nn
# Generate QC to check if vertebrae are aligned
sct_qc -i t2s_subj14_reg.nii.gz -s t2_subj14_crop_r_seg_labeled.nii.gz -p sct_label_vertebrae -qc qc
# Quantify CSA across vertebral levels
sct_process_segmentation -i t2s_subj14_gmseg.nii.gz -vertfile t2_subj14_crop_r_seg_labeled_reg.nii.gz -vert 1:7 -perlevel 1 -o csa_gm.csv
sct_process_segmentation -i t2s_subj14_wmseg.nii.gz -vertfile t2_subj14_crop_r_seg_labeled_reg.nii.gz -vert 1:7 -perlevel 1 -o csa_wm.csv

Here are the resulting CSAs: csa_gm.csv (3.6 KB) csa_wm.csv (3.6 KB)

And here is the QC report: qc.zip (765.3 KB)

This was tested with SCT v5.0.1.

Please note that the GM segmentation needs to be checked and manually corrected if necessary, before computing CSAs.

Let me know if you can reproduce these results.

Best,
Julien

ambaf · November 25, 2020, 9:50am

Hi Julien,

This works perfectly thank you!

Best wishes,
Amba

Mohammed_KHAMAYSA · July 9, 2021, 5:16pm

Dear Julien,

Thank you so much for the consistent support and help

I am working on Gm and Wm segmentation for extracting GM/WM CSA using t2s sequence constructed using 2Dmultiger_ACC sequence [using fslmerge -z tool]. Apparently everything goes smoothly and I get at the end the CSA of Gm/Wm.csv per slice file but with missing of the vertebral levels.

I am not sure if it is a problem with the physical coordinates of the images; I tried many ways to crop the t2* based on the t2 but the result was only the 48 slices on the t2 image where I can’t do vertebral labeling.

I am sure I am using the right pipeline because I used it for analyzing the course data and it worked perfectly; I am attaching the csv files that I get at the end of the analysis;

thank you so much
Best regards
csa_gm.csv (15.1 KB) csa_wm.csv (15.1 KB)

jcohenadad · July 12, 2021, 10:16pm

Hi @Mohammed_KHAMAYSA,

Sorry for the late response. Have you run vertebral labeling on your data?

If you share your analysis script that includes all the commands you ran, we will be able to find out where the problem is.

Julien

Mohammed_KHAMAYSA · July 19, 2021, 11:45am

Hi @jcohenadad
Sorry for the late response. I did vertebral labeling on my data. I am attaching the script I used for the analysis after adapting the stranded
many thanks for taking the time to check it batch_single_subject.sh (7.4 KB) bash script

jcohenadad · July 19, 2021, 3:54pm

Hi,

This line is problematic:

sct_register_multimodal -i /home_local/mkhamays/sct_testing_data/mt/label/template/PAM50_t2s.nii.gz -iseg /home_local/mkhamays/sct_testing_data/mt/label/template/PAM50_wm.nii.gz  -d t2s.nii.gz -dseg t2s_wmseg.nii.gz -param step=1,type=seg,algo=rigid:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz

You cannot use an already-registered PAM50 from the testing data and then run sct_warp_template (which assumes the original PAM50, not the one registered under the testing data).

So in this case, what you want to do is:

sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_wm.nii.gz -d t2s_wmseg.nii.gz -dseg t2s_seg.nii.gz -param step=1,type=im,algo=syn,slicewise=1,iter=5 -initwarp warp_template2t2s.nii.gz -initwarpinv warp_t2s2template.nii.gz

Note that you have the same issue later, at line 116:

sct_register_multimodal -i /home_local/mkhamays/sct_testing_data/mt/label/template/PAM50_t1.nii.gz -iseg /home_local/mkhamays/sct_testing_data/mt/label/template/PAM50_cord.nii.gz  -d dwi_moco_mean.nii.gz -dseg dwi_moco_mean_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp ../t2s/warp_template2t2s.nii.gz -initwarpinv ../t2s/warp_t2s2template.nii.gz

I strongly recommend you do all the tutorials to make sure you understand all the steps involved in the analysis, before modifying the example batch processing script.

I also recommend you keep the flag “-qc” so you can perform convenient QC on your processing.

Please let me know if you have additional questions,
Julien