error in ANTSUseLandmarkImagesToGetAffineTransform for Estimate transfo: straight anat --> template (affine landmark-based) about spinalcordtoolbox

[jcohenadad]

Works with testing/data/errsm_23

[jcohenadad]

Tried with labels: C2-T2 (2-9) (instead of C2-T3: 2-10).

sct_register_to_template.py -i t2_crop.nii.gz -l landmarks_rpi_crop__C2-T2.nii.gz -m segmentation_binary_crop.nii.gz -s superfast -r 0

--> that worked!

[jcohenadad]

Tried with labels: C2-T4 (2-11)

sct_register_to_template.py -i t2_crop.nii.gz -l landmarks_rpi_crop__C2-T4.nii.gz -m segmentation_binary_crop.nii.gz -s superfast -r 0

--> that crashed!

ERROR!!! 
fix-label 21 movlabel 21
labels do not match -- exiting 
Exit program.

So it looks like it is not possible to input labels bigger than 9. This needs to be fixed

[jcohenadad]

Created labels with itksnap. And checked with:

sct_label_utils.py -i label_itksnap.nii.gz -t display-voxel

Values are now:

Position=(49,192,249) -- Value= 24
Position=(51,191,105) -- Value= 104
Position=(56,186,249) -- Value= 23
Position=(56,187,105) -- Value= 103
Position=(56,194,105) -- Value= 101
Position=(56,196,249) -- Value= 21
Position=(62,191,105) -- Value= 102
Position=(64,191,249) -- Value= 22

Instead of:

Position=(49,189,104) -- Value= 104.0
Position=(49,190,104) -- Value= 104.0
Position=(49,190,255) -- Value= 24.0
Position=(49,191,104) -- Value= 104.0
Position=(49,191,255) -- Value= 24.0
Position=(49,192,255) -- Value= 24.0
Position=(50,189,104) -- Value= 104.0
Position=(50,190,104) -- Value= 104.0
Position=(50,190,255) -- Value= 24.0
Position=(50,191,104) -- Value= 104.0
...

So the ".0" at the end seems to make the difference.

[jcohenadad]

Investigating datatype:
fslhd gives:

• label_itksnap: UINT16
• landmarks_rpi_cross3x3: INT32
• landmarks_rpi_cross3x3_straight.nii.gz: FLOAT32
• template_label_cross.nii.gz: INT32
• template_label.nii.gz: UINT32

[jcohenadad]

Changed output datatype for UINT16. Command ran:

c3d ../t2_crop.nii.gz -o data.nii
c3d ../landmarks_rpi_crop.nii.gz -o landmarks.nii
c3d ../segmentation_binary_crop.nii.gz -o segmentation.nii
sct_orientation -i data.nii -o data_rpi.nii.gz -orientation RPI
sct_orientation -i landmarks.nii.gz -o landmarks_rpi.nii.gz -orientation RPI
sct_orientation -i segmentation.nii.gz -o segmentation_rpi.nii.gz -orientation RPI
sct_straighten_spinalcord.py -i data_rpi.nii.gz -c segmentation_rpi.nii.gz -r 1
sct_label_utils.py -t remove -i ${SCT_DIR}/data/template/landmarks_center.nii.gz -o template_label.nii.gz -r landmarks_rpi.nii.gz
sct_label_utils.py -t cross -i template_label.nii.gz -o template_label_cross.nii.gz -c 5
sct_label_utils.py -t cross -i landmarks_rpi.nii.gz -o landmarks_rpi_cross3x3.nii.gz -c 5 -d
WarpImageMultiTransform 3 landmarks_rpi_cross3x3.nii.gz landmarks_rpi_cross3x3_straight.nii.gz -R data_rpi_straight.nii.gz warp_curve2straight.nii.gz --use-NN
ANTSUseLandmarkImagesToGetAffineTransform template_label_cross.nii.gz landmarks_rpi_cross3x3_straight.nii.gz affine tmp.straight2templateAffine.txt

error:

 fix-label 21 movlabel 21
 labels do not match -- exiting 

datatypes are:

• landmarks_rpi_cross3x3: UINT16
• landmarks_rpi_cross3x3_straight.nii.gz: FLOAT32
• template_label_cross.nii.gz: UINT16
• template_label.nii.gz: UINT16