Closed sandrinebedard closed 3 weeks ago
tagging @jcohenadad @valosekj @mguaypaq @NathanMolinier
Looks good to me! (i'm copy/pasting in case the issue text changes in the future)
Note: do we want to add the discs labels from warping from T2w for the other contrasts inside the derivatives? (as we do and need for the contrast-agnostic project)
I would say yes, so that the contrast-agnostic model can more easily be reproduced, no?
so that the contrast-agnostic model can more easily be reproduced, no?
Yes! We required the disc labels for vertebral labeling and the C2-C3 CSA computation via sct_process_segmentation
. Hence, adding the disc labels would be good!
@NathanMolinier
We have some disc labels that are warped from the T2w, but we want to add them in the derivatives 2 (BUT THEY MAY NOT BE PERFECT) and we do not want to be confused between them and manual disc labels, do you have a suggetsion?
We should also add the space-other
field https://github.com/spine-generic/data-multi-subject/issues/156
I noticed that the disc labels in the derivatives are in the original space LPI, should I reorient them and add space-other
to be consitent? or do we keep them in the original space?
We should also add the
space-other
field #156
Or space-warp
but we need to add this to the JSON sidecar as well to say that the image was warped from another contrast
I noticed that the disc labels in the derivatives are in the original space LPI, should I reorient them and add
space-other
to be consitent? or do we keep them in the original space?
Therefore, do we need to store 2 versions of the discs labels ?
reorientation is a very simple step, I don't think we need 2 versions (in the contrast-agnsotic pipeline, sct_label_vertebrae reorients in any case)
Description
Since we have now clarified the naming of the labels in the derivatives, we need to update the derivatives name in spine generic
Suggestions
sub-amu01_T2star_seg-manual.nii.gz
-->sub-amu01_T2star_label-SC_seg.nii.gz
sub-amu01_T2w_labels-disc-manual.nii.gz
-->sub-amu01_T2w_label-discs_dlabel.nii.gz
sub-amu01_T1w_softseg.nii.gz
-->sub-amu01_T1w_label-SC_softseg.nii.gz
sub-amu01_T1w_softseg_bin.nii.gz
-->sub-amu01_T1w_desc-softseg_label-SC_seg.nii.gz
(to be discussed)sub-amu01_T1w_csfseg-manual.nii.gz
-->sub-amu01_T1w_label-CSF_seg.nii.gz
sub-amu01_T2w_label-discs_desc-warp_dlabel.nii.gz
_RPI_r_labels-manual
-->space-other_T2w_label-vertebrae_desc-C2C5_dlabel
gmseg
-->label-GM_seg
Note: do we want to add the discs labels from warping from T2w for the other contrasts inside the derivatives? (as we do and need for the contrast-agnostic project)
Related issues
156
154
141
TODO