Differences in CSA

Hello guys!
I am running CSA analysis for different studies, but recently I came across with a potential issue; when I analyze some nii the majority of the CSA in the cervical spinal cord are in magnitude of 10s (ie C3 45) but with one study I am finding magnitudes of 100 (ie 900). Can someone give me some orientation of what is happening?

Hi @enriquegf,

Thank you for reaching out. Could you please clarify what you mean by “10s (ie C3 45)”? CSA are in mm^2, so I am not sure what you meant here.

I’m also confused by “magnitudes of 100 (ie 900)”. What is the unit here? And what does “ie 900” mean?

I am sorry for this barely legible explanation. I upload both screenshot from what I ve done.

Captura de Pantalla 2021-01-27 a la(s) 9.38.41 Captura de Pantalla 2021-01-27 a la(s) 9.38.51

I obtained results from one study in magnitude of hundreds, but in the same patient in a previous study it is in magnitude of tens.

It is probably caused by your NIfTI headers, which are corrupted (ie: the qform/sform does not reflect the actual physical dimensions). If you upload an example image and segmentation that yields those CSAs I can have a look.

ok! here is the .nii of this patient from which I obtained this results.
Thank very very much! I am just beginning to try SCT as a neurologist m20.nii.gz (2.4 MB)

hum, the header looks good-- could you please also upload the segmentation you used to compute the CSA?

Of course! here it is

m20_seg_labeled_discs.nii.gz (77.7 KB) m20_seg_labeled.nii.gz (84.3 KB) m20_seg.nii.gz (4.8 KB)

I’m not sure what you did, but results look OK on my end:

VertLevel MEAN(area)
8 44.05825885019590
7 48.594102619341700
6 53.87744611037150
5 63.68126638238550
4 57.07686534077420
3 57.532144223958000

CSV output: csa.csv (2.9 KB)

I used this command (SCT v5.1.0):

sct_process_segmentation -i m20_seg.nii.gz -vertfile m20_seg_labeled.nii.gz -vert 3:8 -perlevel 1

Thanks!
I will re-run it to try to look for what error I might have.

If you could write the exact syntax you typed it is helpful for us to debug. Usually we ask users to copy/paste the syntax and output from the Terminal.

Hi @enriquegf, just following up to see if you still have an issue, or if we can close this ticket?

no news from the user after one month so I’m tagging this issue as “solved”

I am sorry for the delay Prof. Cohen,

I have been re running this same analysis and found again the same situation. In this occasion I will paste the text:

MacBook-QQ:t2_tse_sag_320_16 enriquegomezfigueroa$ sct_propseg -i m21.nii.gz -c t2


Spinal Cord Toolbox (4.3)

Create temporary folder (/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314112256.300851-label_vertebrae-0pqrzedw)…
Remove temporary files…
rm -rf /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314112256.305088-7059gwqu
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_propseg -t t2 -o ./ -verbose -i ‘/Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16/m21.nii.gz’ -init-centerline /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314112256.300851-label_vertebrae-0pqrzedw/centerline_optic.nii.gz -centerline-binary # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16

Check consistency of segmentation…

Create temporary folder (/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314112326.853661-propseg-ym5n60am)…
tmp.segmentation.nii.gz
tmp.centerline.nii.gz

Get data dimensions…
usage: sct_image -i [ …] [-h] [-o ] [-pad ]
[-pad-asym ] [-split {x,y,z,t}] [-concat {x,y,z,t}]
[-remove-vol ] [-keep-vol ]
[-type {uint8,int16,int32,float32,complex64,float64,int8,uint16,uint32,int64,uint64}]
[-copy-header ] [-getorient]
[-setorient {RIP,LIP,RSP,LSP,RIA,LIA,RSA,LSA,IRP,ILP,SRP,SLP,IRA,ILA,SRA,SLA,RPI,LPI,RAI,LAI,RPS,LPS,RAS,LAS,PRI,PLI,ARI,ALI,PRS,PLS,ARS,ALS,IPR,SPR,IAR,SAR,IPL,SPL,IAL,SAL,PIR,PSR,AIR,ASR,PIL,PSL,AIL,ASL}]
[-setorient-data {RIP,LIP,RSP,LSP,RIA,LIA,RSA,LSA,IRP,ILP,SRP,SLP,IRA,ILA,SRA,SLA,RPI,LPI,RAI,LAI,RPS,LPS,RAS,LAS,PRI,PLI,ARI,ALI,PRS,PLS,ARS,ALS,IPR,SPR,IAR,SAR,IPL,SPL,IAL,SAL,PIR,PSR,AIR,ASR,PIL,PSL,AIL,ASL}]
[-mcs] [-omc] [-display-warp] [-to-fsl [ [ …]]]
[-v {0,1,2}]
sct_image: error: unrecognized arguments: Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16/m21_seg.nii.gz
MacBook-QQ:t2_tse_sag_320_16 enriquegomezfigueroa$ sct_label_vertebrae -i m21.nii.gz -s m21_seg.nii.gz -c t2


Spinal Cord Toolbox (4.3)

Create temporary folder (/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.857435-label_vertebrae-ti9i761j)…

Copying input data to tmp folder…

Straighten spinal cord…

Create temporary folder (/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.960104-straighten_spinalcord-14jub3zi)…

Copy files to tmp folder…
Window length needs to be >= 3. Returning input signal.
Window length needs to be >= 3. Returning input signal.
Fitting centerline using B-spline approximation
Error on approximation = 24.28 mm
Error on approximation = 5.47 mm
Error on approximation = 5.46 mm
Error on approximation = 2.85 mm
Error on approximation = 1.25 mm
Error on approximation = 0.56 mm
Error on approximation = 0.36 mm
Error on approximation = 0.38 mm
Error on approximation = 0.42 mm
Error on approximation = 0.32 mm
Error on approximation = 0.22 mm
Error on approximation = 0.22 mm
Error on approximation = 0.24 mm
Error on approximation = 0.19 mm
Error on approximation = 0.19 mm
Error on approximation = 0.2 mm
Error on approximation = 0.2 mm
Error on approximation = 0.17 mm
Error on approximation = 0.17 mm
Error on approximation = 0.17 mm
Error on approximation = 0.16 mm
Error on approximation = 0.1 mm
Error on approximation = 0.06 mm
Error on approximation = 0.06 mm
Error on approximation = 0.09 mm
Error on approximation = 0.09 mm
Error on approximation = 0.07 mm
Error on approximation = 0.06 mm
Error on approximation = 0.05 mm
Error on approximation = 0.05 mm
Error on approximation = 0.05 mm
Create the straight space and the safe zone
Length of spinal cord: 235.5724424780292
Size of spinal cord in z direction: 219.3125
Ratio length/size: 1.0741405185661064
Safe zone boundaries (curved space): [-157.9805145263672, 61.33198547363281]
Safe zone boundaries (straight space): [-166.11048576538178, 69.46195671264742]
Pad input volume to account for spinal cord length…
Time to generate centerline: 41.0 ms
100%|████████████████████████████████████████| 344/344 [00:01<00:00, 190.79it/s]
100%|█████████████████████████████████████████| 356/356 [00:09<00:00, 37.02it/s]
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image…
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -r tmp.centerline_pad_crop.nii.gz -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -n ‘BSpline[3]’ # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.960104-straighten_spinalcord-14jub3zi
Generate output files…
File created: ./warp_curve2straight.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.960104-straighten_spinalcord-14jub3zi/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
File created: ./data_straight.nii
Remove temporary files…
rm -rf /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.960104-straighten_spinalcord-14jub3zi

Finished! Elapsed time: 48 s

Done! To view results, type:
fsleyes ./data_straight.nii &

Resample to 0.5mm isotropic…
sct_resample -i data_straight.nii -mm 0.5x0.5x0.5 -x linear -o data_straightr.nii # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.857435-label_vertebrae-ti9i761j

Apply straightening to segmentation…
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -r data_straightr.nii -t warp_curve2straight.nii.gz -o segmentation_straight.nii -n Linear # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.857435-label_vertebrae-ti9i761j
sct_maths -i segmentation_straight.nii -thr 0.5 -o segmentation_straight.nii # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.857435-label_vertebrae-ti9i761j

Create label to identify disc…
Creating temporary folder…
Run C2-C3 detector…
C2-C3 detected…
Remove temporary files…
rm -rf /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113444.854512-ld0ifbh4
File /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.857435-label_vertebrae-ti9i761j/labelz.nii.gz already exists. Will overwrite it.

And apply straightening to label…
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i labelz.nii.gz -r data_straightr.nii -t warp_curve2straight.nii.gz -o labelz_straight.nii.gz -n NearestNeighbor # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.857435-label_vertebrae-ti9i761j

Get z and disc values from straight label…
… [255, 3]

Look for template…
Path template: /Users/enriquegomezfigueroa/sct_4.3/data/PAM50

Open template and vertebral levels…

Disc values from template: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
Z-values for each disc: [962, 939, 908, 871, 834, 801, 770, 736, 693, 647, 601, 552, 501, 450, 397, 343, 290, 232, 169, 106, 56]
Distances between discs (in voxel): [23.0, 31.0, 37.0, 37.0, 33.0, 31.0, 34.0, 43.0, 46.0, 46.0, 49.0, 51.0, 51.0, 53.0, 54.0, 53.0, 58.0, 63.0, 63.0, 50.0]

Detect intervertebral discs…
Current disc: 2 (z=255). Direction: superior
… Peak found: z=7 (correlation = 0.3446798129799675)
Current disc: 1 (z=293). Direction: superior
… correcting factor: 1.0
… Switching to inferior direction.
Current disc: 3 (z=218). Direction: inferior
… Peak found: z=-4 (correlation = 0.426649759126742)
… correcting factor: 1.1486486486486487
Current disc: 4 (z=172). Direction: inferior
… Peak found: z=-3 (correlation = 0.35060838465960964)
… correcting factor: 1.1711711711711712
Current disc: 5 (z=130). Direction: inferior
… Peak found: z=2 (correlation = 0.3879841966324763)
… correcting factor: 1.1586814086814088
Current disc: 6 (z=96). Direction: inferior
… Peak found: z=6 (correlation = 0.5028242869773111)
… correcting factor: 1.1204935140419012
Current disc: 7 (z=64). Direction: inferior
… Peak found: z=5 (correlation = 0.5461460531736383)
… correcting factor: 1.0955093009172707
Current disc: 8 (z=22). Direction: inferior
… Peak found: z=8 (correlation = 0.532315569367595)
… correcting factor: 1.0685760785270957
Adding top disc based on adjusted template distance: #0
… approximate distance: 25

Un-straighten labeling…
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i segmentation_straight_labeled.nii -r segmentation.nii -t warp_straight2curve.nii.gz -o segmentation_labeled.nii -n NearestNeighbor # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.857435-label_vertebrae-ti9i761j

Clean labeled segmentation (correct interpolation errors)…
File /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.857435-label_vertebrae-ti9i761j/segmentation_labeled.nii already exists. Will overwrite it.

Label discs…

Generate output files…
File created: ./m21_seg_labeled.nii.gz
File created: ./m21_seg_labeled_discs.nii.gz
File created: ./warp_curve2straight.nii.gz
File created: ./warp_straight2curve.nii.gz
File created: ./straight_ref.nii.gz

Remove temporary files…
rm -rf /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314113350.857435-label_vertebrae-ti9i761j

Done! To view results, type:
fsleyes /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16/m21.nii.gz -a 100.0 ./m21_seg_labeled.nii.gz -cm subcortical -a 50.0 &

MacBook-QQ:t2_tse_sag_320_16 enriquegomezfigueroa$ sct_register_to_template -i m21.nii.gz -s m21_seg.nii.gz -l m21_seg_labeled.nii.gz -c t2


Spinal Cord Toolbox (4.3)

Check template files…
OK: /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_t2.nii.gz
OK: /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_levels.nii.gz
OK: /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_cord.nii.gz

Check parameters:
Data: m21.nii.gz
Landmarks: m21_seg_labeled.nii.gz
Segmentation: m21_seg.nii.gz
Path template: /Users/enriquegomezfigueroa/sct_4.3/data/PAM50
Remove temp files: 1

Check input labels…
ERROR: Label file has 3231 label(s). It must contain one or two labels.
ERROR: Found two labels with same value.

Create temporary folder (/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk)…

Copying input data to tmp folder and convert to nii…

Generate labels from template vertebral labeling
Value = 1 : (70.0, 70.0505921918409, 951.0333382073403) --> ( 70.0, 70.0, 951.0)
Value = 2 : (70.0, 70.30833886308339, 923.9948020349481) --> ( 70.0, 70.0, 924.0)
Value = 3 : (70.0, 70.50121918179356, 889.7335862006682) --> ( 70.0, 71.0, 890.0)
Value = 4 : (70.0, 70.38403779633848, 852.8857673162912) --> ( 70.0, 70.0, 853.0)
Value = 5 : (70.0, 70.30789525112371, 818.2217119405902) --> ( 70.0, 70.0, 818.0)
Value = 6 : (70.0, 70.7014333993707, 786.225032047547) --> ( 70.0, 71.0, 786.0)
Value = 7 : (70.0, 70.80759724209705, 753.9094575256927) --> ( 70.0, 71.0, 754.0)
Value = 8 : (70.0, 70.35343403351428, 715.2977342459287) --> ( 70.0, 70.0, 715.0)
Value = 9 : (70.0, 70.41839798246667, 670.7036147472079) --> ( 70.0, 70.0, 671.0)
Value = 10 : (70.0, 70.41868823000898, 624.8615068668977) --> ( 70.0, 70.0, 625.0)
Value = 11 : (70.0, 70.43996427204287, 577.066096720684) --> ( 70.0, 70.0, 577.0)
Value = 12 : (70.0, 70.4400396432111, 527.0463330029733) --> ( 70.0, 70.0, 527.0)
Value = 13 : (70.0, 70.48122739179244, 475.89622053137083) --> ( 70.0, 70.0, 476.0)
Value = 14 : (70.0, 70.57302038880987, 424.0064011379801) --> ( 70.0, 71.0, 424.0)
Value = 15 : (70.0, 70.64169901804065, 370.32187714089974) --> ( 70.0, 71.0, 370.0)
Value = 16 : (70.0, 70.69621109607577, 316.83818222823635) --> ( 70.0, 71.0, 317.0)
Value = 17 : (70.0, 70.5720703125, 261.3439453125) --> ( 70.0, 71.0, 261.0)
Value = 18 : (70.0, 70.67006390034781, 200.1311979293052) --> ( 70.0, 71.0, 200.0)
Value = 19 : (70.0, 70.47842956120093, 141.44073903002308) --> ( 70.0, 70.0, 141.0)
Value = 20 : (70.0, 70.68440271257172, 92.52008346374544) --> ( 70.0, 71.0, 93.0)

Check if provided labels are available in the template

Binarize segmentation

Done! To view results, type:
fsleyes seg_bin.nii.gz &

Resample data to 1mm isotropic…
load data…

Done! To view results, type:
fsleyes data_1mm.nii &

load data…

Done! To view results, type:
fsleyes seg_bin_1mm.nii.gz &

Position=(149,207,6) – Value= 1
Position=(144,188,6) – Value= 2
Position=(139,161,6) – Value= 3
Position=(139,129,6) – Value= 4
Position=(146,102,5) – Value= 5
Position=(157,79,5) – Value= 6
Position=(170,58,5) – Value= 7
Position=(186,33,5) – Value= 8
Position=(199,10,5) – Value= 9
All labels (useful syntax):
149,207,6,1:144,188,6,2:139,161,6,3:139,129,6,4:146,102,5,5:157,79,5,6:170,58,5,7:186,33,5,8:199,10,5,9
sct_label_utils -i data_1mm.nii -create 102,142,20,1:99,129,20,2:96,111,20,3:96,89,20,4:100,70,17,5:108,54,17,6:117,40,17,7:128,23,17,8:137,7,17,9 -v 1 -o label_projected_1mm.nii.gz # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk

Change orientation of input images to RPI…

Straighten the spinal cord using centerline/segmentation…

Create temporary folder (/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114150.213562-straighten_spinalcord-7rhmvmrd)…

Copy files to tmp folder…
Create the straight space and the safe zone
Length of spinal cord: 234.76689547312802
Size of spinal cord in z direction: 219.0
Ratio length/size: 1.0719949564983013
Safe zone boundaries (curved space): [-157.9805145263672, 61.01948547363281]
Safe zone boundaries (straight space): [-165.86396226293118, 68.9029332101968]
Pad input volume to account for spinal cord length…
Time to generate centerline: 29.0 ms
100%|█████████████████████████████████████████| 236/236 [00:05<00:00, 41.41it/s]
100%|█████████████████████████████████████████| 244/244 [00:10<00:00, 23.61it/s]
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image…
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -r tmp.centerline_pad_crop.nii.gz -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -n ‘BSpline[3]’ # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114150.213562-straighten_spinalcord-7rhmvmrd
Generate output files…
File created: ./warp_curve2straight.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114150.213562-straighten_spinalcord-7rhmvmrd/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
File created: /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/seg_bin_1mm_rpi_crop_straight.nii.gz
Remove temporary files…
rm -rf /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114150.213562-straighten_spinalcord-7rhmvmrd

Parse list of warping fields…

Check file existence…
OK: /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/data_1mm_rpi.nii
OK: warp_straight2curve.nii.gz
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/data_1mm_rpi.nii warp_straight2curve.nii.gz # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk

Generate output files…
WARNING: File warp_straight2curve.nii.gz already exists. Deleting it…
File created: warp_straight2curve.nii.gz

Remove unused label on template. Keep only label present in the input label image…
sct_label_utils -i template_label_body.nii.gz -o template_label_body.nii.gz -remove-reference /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/label_projected_1mm_rpi.nii.gz # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk

Dilating input labels using 3vox ball radius

Apply straightening to labels…

Parse list of warping fields…

Get dimensions of data…
43 x 220 x 220 x 1

Apply transformation…

Apply transformation and resample to destination space…
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/label_projected_1mm_rpi_dilate.nii.gz -o /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/label_projected_1mm_rpi_dilate_straight.nii.gz -t warp_curve2straight.nii.gz -r /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/seg_bin_1mm_rpi_crop_straight.nii.gz -n NearestNeighbor # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk
Copy affine matrix from destination space to make sure qform/sform are the same.

Done! To view results, type:
fsleyes /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/seg_bin_1mm_rpi_crop_straight.nii.gz /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/label_projected_1mm_rpi_dilate_straight.nii.gz &

Estimate transformation for step #0
Labels src: [[-1.107864217544961, 5.8457866761742565, -17.882953550757435], [-3.3371592878478857, 6.338770304640676, -31.555856992120624], [-3.2265677633285534, 6.852030578613281, -50.77251452636719], [-4.241870142573077, 7.1568938879657935, -74.73591020982043], [-1.9794924143141372, 6.236030578613281, -94.98051452636719], [-2.342063518627633, 6.2643324654057295, -111.95221263957473], [-2.3326514959335327, 6.541293736508024, -127.28577768426192], [-2.3589060855539223, 6.771118297911528, -145.77876014040228], [-2.3185997437423396, 6.510678465937218, -162.54389480805733]]
Labels dest: [[-0.0, 46.220001220703125, -86.34002685546875], [-0.0, 46.220001220703125, -99.84002685546875], [-0.0, 45.720001220703125, -116.84002685546875], [-0.0, 46.220001220703125, -135.34002685546875], [-0.0, 46.220001220703125, -152.84002685546875], [-0.0, 45.720001220703125, -168.84002685546875], [-0.0, 45.720001220703125, -184.84002685546875], [-0.0, 46.220001220703125, -204.34002685546875], [-0.0, 46.220001220703125, -226.34002685546875]]
Degrees of freedom (dof): Tx_Ty_Tz_Sz
Optimization terminated successfully.
Current function value: 112.899859
Iterations: 2
Function evaluations: 159
Matrix:
[[ 1. 0. 0.]
[ 0. 1. 0.]
[-0. 0. 1.]]
Center:
[ 0. 46.05333455 -152.84002686]
Translation:
[[ -2.58279717 -39.55145289 62.00798296]]

Concatenate transformations: curve --> straight --> affine…

Parse list of warping fields…

Check file existence…
OK: template.nii
OK: warp_curve2straight.nii.gz
OK: straight2templateAffine.txt
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R template.nii straight2templateAffine.txt warp_curve2straight.nii.gz # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk

Generate output files…
File created: warp_curve2straightAffine.nii.gz

Apply transformation…

Parse list of warping fields…

Get dimensions of data…
43 x 220 x 220 x 1

Apply transformation…

Apply transformation and resample to destination space…
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/data_1mm_rpi.nii -o /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/data_1mm_rpi_straightAffine.nii -t warp_curve2straightAffine.nii.gz -r template.nii -n ‘BSpline[3]’ # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk
Copy affine matrix from destination space to make sure qform/sform are the same.

Done! To view results, type:
fsleyes template.nii /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/data_1mm_rpi_straightAffine.nii &

Parse list of warping fields…

Get dimensions of data…
43 x 220 x 220 x 1

Apply transformation…

Apply transformation and resample to destination space…
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/seg_bin_1mm_rpi_crop.nii.gz -o /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/seg_bin_1mm_rpi_crop_straightAffine.nii.gz -t warp_curve2straightAffine.nii.gz -r template.nii -n Linear # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk
Copy affine matrix from destination space to make sure qform/sform are the same.

Done! To view results, type:
fsleyes template.nii /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/seg_bin_1mm_rpi_crop_straightAffine.nii.gz &

Part II:

Crop data in template space (for faster processing)…

Sub-sample in z-direction (for faster processing)…
sct_resample -i template_crop.nii -o template_crop_sub.nii -f 1x1x0.25 # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk
sct_resample -i template_seg_crop.nii.gz -o template_seg_crop_sub.nii.gz -f 1x1x0.25 # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk
sct_resample -i /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/data_1mm_rpi_straightAffine_crop.nii -o /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/data_1mm_rpi_straightAffine_crop_sub.nii -f 1x1x0.25 # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk
sct_resample -i /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/seg_bin_1mm_rpi_crop_straightAffine_crop.nii.gz -o /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk/seg_bin_1mm_rpi_crop_straightAffine_crop_sub.nii.gz -f 1x1x0.25 # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk

Register straight spinal cord to template…

Create temporary folder (/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0)…

Copying input data to tmp folder and convert to nii…


ESTIMATE TRANSFORMATION FOR STEP #1
Registration parameters:
type … imseg
algo … centermassrot
slicewise … 0
metric … MeanSquares
iter … 10
smooth … 0
laplacian … 0
shrink … 1
gradStep … 0.5
deformation … 1x1x0
init …
poly … 5
filter_size … 5
dof … Tx_Ty_Tz_Rx_Ry_Rz
smoothWarpXY … 2
rot_method … pcahog

Create temporary folder (/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114244.216976-register-t7d5oadw)…

Copy input data to temp folder…
sct_convert -i src.nii -o /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114244.216976-register-t7d5oadw/src.nii
sct_convert -i src_seg.nii -o /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114244.216976-register-t7d5oadw/src_seg.nii
sct_convert -i dest_RPI.nii -o /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114244.216976-register-t7d5oadw/dest.nii
sct_convert -i dest_seg_RPI.nii -o /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114244.216976-register-t7d5oadw/dest_seg.nii

Get image dimensions of destination image…
matrix size: 141 x 141 x 80
voxel size: 0.5mm x 0.5mm x 1.99375mm

Split input segmentation…

Split destination segmentation…

Split input image…

Split destination image…
Estimate cord angle for each slice: 0%| | 0/80 [00:00<?, ?iter/s]Switched to method ‘hog’ for slice: 0
Estimate cord angle for each slice: 1%|▎ | 1/80 [00:00<00:42, 1.88iter/s]Switched to method ‘hog’ for slice: 1
Switched to method ‘hog’ for slice: 3
Switched to method ‘hog’ for slice: 4
Estimate cord angle for each slice: 6%|█▋ | 5/80 …

Generate warping field…
–> step1Warp.nii.gz

Generate warping field…
–> step1InverseWarp.nii.gz

Move warping fields…
cp step1Warp.nii.gz /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0
cp step1InverseWarp.nii.gz /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0
rm -rf /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114244.216976-register-t7d5oadw


ESTIMATE TRANSFORMATION FOR STEP #2

Apply transformation from previous step

Parse list of warping fields…

Get dimensions of data…
141 x 141 x 80 x 1

Apply transformation…

Apply transformation and resample to destination space…
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0
Copy affine matrix from destination space to make sure qform/sform are the same.

Done! To view results, type:
fsleyes dest_seg_RPI.nii src_seg_reg.nii &

Registration parameters:
type … seg
algo … bsplinesyn
slicewise … 0
metric … MeanSquares
iter … 3
smooth … 1
laplacian … 0
shrink … 1
gradStep … 0.5
deformation … 1x1x0
init …
poly … 5
filter_size … 5
dof … Tx_Ty_Tz_Rx_Ry_Rz
smoothWarpXY … 2
rot_method … pca
sct_image -i dest_seg_RPI.nii -o dest_seg_RPI_pad.nii -pad 0,0,10 # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0

Estimate transformation
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsRegistration --dimensionality 3 --transform ‘bsplinesyn[0.5,1,3]’ --metric ‘MeanSquares[dest_seg_RPI_pad.nii,src_seg_reg.nii,1,4]’ --convergence 3 --shrink-factors 1 --smoothing-sigmas 1mm --restrict-deformation 1x1x0 --output ‘[step2,src_seg_reg_regStep2.nii]’ --interpolation ‘BSpline[3]’ --verbose 1 # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0

Concatenate transformations…

Parse list of warping fields…

Check file existence…
OK: dest.nii
OK: warp_forward_1.nii.gz
OK: warp_forward_2.nii.gz
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0

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_inverse_1.nii.gz
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R src.nii warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0

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 80 x 1

Apply transformation…

Apply transformation and resample to destination space…
/Users/enriquegomezfigueroa/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 /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0
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…
141 x 141 x 80 x 1

Apply transformation…

Apply transformation and resample to destination space…
/Users/enriquegomezfigueroa/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 /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0
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: data_1mm_rpi_straightAffine_crop_sub_reg.nii
File created: template_crop_sub_reg.nii
File created: warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz
File created: warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz

Remove temporary files…
rm -rf /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114243.804847-register-c7703qd0

Concatenate transformations: anat --> template…

Parse list of warping fields…

Check file existence…
OK: template.nii
OK: warp_curve2straightAffine.nii.gz
OK: warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R template.nii warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz warp_curve2straightAffine.nii.gz # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk

Generate output files…
File created: warp_anat2template.nii.gz

Concatenate transformations: template --> anat…

Parse list of warping fields…

Check file existence…
OK: data.nii
OK: warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz
OK: straight2templateAffine.txt
OK: warp_straight2curve.nii.gz
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R data.nii warp_straight2curve.nii.gz -i straight2templateAffine.txt warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk

Generate output files…
File created: warp_template2anat.nii.gz
sct_apply_transfo -i template.nii -o template2anat.nii.gz -d data.nii -w warp_template2anat.nii.gz -crop 0 # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk
sct_apply_transfo -i data.nii -o anat2template.nii.gz -d template.nii -w warp_anat2template.nii.gz -crop 0 # in /private/var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk

Generate output files…
File created: warp_template2anat.nii.gz
File created: warp_anat2template.nii.gz
File created: template2anat.nii.gz
File created: anat2template.nii.gz
WARNING: File warp_curve2straight.nii.gz already exists. Deleting it…
File created: warp_curve2straight.nii.gz
WARNING: File warp_straight2curve.nii.gz already exists. Deleting it…
File created: warp_straight2curve.nii.gz
WARNING: File straight_ref.nii.gz already exists. Deleting it…
File created: straight_ref.nii.gz

Delete temporary files…
rm -rf /var/folders/wg/9vmplq4s7llbcbtzm6y4wpsr0000gn/T/sct-20210314114141.330551-register_to_template-be2y71zk

Finished! Elapsed time: 189s

Done! To view results, type:
fsleyes m21.nii.gz template2anat.nii.gz &

Done! To view results, type:
fsleyes /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz &

MacBook-QQ:t2_tse_sag_320_16 enriquegomezfigueroa$ sct_warp_template -d m21.nii.gz -w warp_template2anat.nii.gz -a 0


Spinal Cord Toolbox (4.3)

Check parameters:
Working directory … /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
Destination image … m21.nii.gz
Warping field … warp_template2anat.nii.gz
Path template … /Users/enriquegomezfigueroa/sct_4.3/data/PAM50
Output folder … label

WARP TEMPLATE:
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_t1.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_t1.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_t2.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_t2.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_t2s.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_t2s.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_cord.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_cord.nii.gz -n NearestNeighbor # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_wm.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_wm.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_gm.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_gm.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_csf.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_csf.nii.gz -n NearestNeighbor # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_levels.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_levels.nii.gz -n NearestNeighbor # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_levels_continuous.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_label_body.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_label_body.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_label_disc.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_label_disc.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_label_discPosterior.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_spine.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_spine.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_centerline.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_centerline.nii.gz -n Linear # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
/Users/enriquegomezfigueroa/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -r m21.nii.gz -t warp_template2anat.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -n NearestNeighbor # in /Users/enriquegomezfigueroa/Desktop/Machado Ancona Eugenia/M21/Machado_Ancona_Eugenia_Margarita/Craneo_Cerebro_2017 - 1/t2_tse_sag_320_16
cp /Users/enriquegomezfigueroa/sct_4.3/data/PAM50/template/info_label.txt label/template

Done! To view results, type:
fsleyes m21.nii.gz -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 &

This is the file I was trying to analyze m21.nii.gz (1.5 MB)

hi,

this is what i’ve done:

# segment cord
sct_deepseg_sc -i m21.nii.gz -c t2 -qc qc
# segment vertebral levels
sct_label_vertebrae -i m21.nii.gz -s m21_seg.nii.gz -c t2 -qc qc
# compute CSA per level
sct_process_segmentation -i m21_seg.nii.gz -vert 3:8 -perlevel 1 -vertfile m21_seg_labeled.nii.gz -o csa.csv

Output CSA:

Slice (I->S) VertLevel MEAN(area)
59:79 7 44.588012478803200
80:98 6 49.05501984303600
99:125 5 56.86860001785900
126:146 4 60.863621026422700
147:168 3 47.8760699285787
169:189 2 58.94214593820830

Output CSV: csa.csv (3.0 KB)

Output QC: qc.zip (886.8 KB)

Two things to note:

  1. Computing CSA on sagittal images with very thick sliced (3.3mm here) is inaccurate and hence not recommended
  2. In the QC you will notice slight mis-labeling of the vertebral level. If that happens, you can fix it using the command sct_label_utils to label the discs of interest, and then run sct_label_vertebrae -discfile. Example here:

Thank you very much Prof. Cohen,

Just to be clear what I usually do is this:

  1. sct_propseg -i t2.nii.gz -c t2
  2. sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2
  3. sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_seg_labeled.nii.gz -c t2
  4. sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0
  5. sct_process_segmentation -i t2_seg.nii.gz -vert 3:8 -perlevel 1 -o csa_c3c4.csv

So I should #segment cord (deepest_sc) in step 2?

Hi,

in my previous comment Differences in CSA i forgot to add the line with “sct_process_segmentation”. It is now added.

So I should #segment cord (deepest_sc) in step 2?

What I am suggesting is that you bypass registration to template if you don’t need it. And you can do the segmentation of the cord with sct_propseg or sct_deepseg_sc, based on what you find gives the best results.

Again, I’ve updated the code for you in Differences in CSA.

It is 3 lines of code.

Run it, let me know if it works for you.