Closed uzaymacar closed 11 months ago
To me this is a limitation of ivadomed
and the problem needs to be fixed there, sooner rather than later. Ongoing discussions:
Below are the BIDS-compliant files we need to support (on the right) and their older names (on the left) as mentioned in https://github.com/spine-generic/data-multi-subject/issues/116:
acq-MTon_MTS → flip-1_mt-on_MTS
acq-MToff_MTS → flip-1_mt-off_MTS
acq-T1w_MTS → flip-2_mt-off_MTS
The issue with the ivadomed loader will be addressed here: https://github.com/ivadomed/ivadomed/pull/1240
Once fixed, please edit README: https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/blob/main/README.md#dataset
I see that the file names have been changed but not updated in the ReadMe yet. @sandrinebedard could you please briefly describe it in the ReadMe? Thanks!
I removed all instances of training with ivadomed, where is mentionned the MTS contrasts:
The
spine-generic-processed
dataset includeacq-MTon_MTS
andacq-T1w_MTS
contrast. As noted in the previous meeting, these contrasts were not picked bypybids==0.15.1
. We discovered two solutions to the problem:force_index
similar to how it is done for microscopy and CT at these linespybids==0.15.2
which introducedMTS
support and rename the files according to https://github.com/spine-generic/data-multi-subject/issues/116.However, in both of these solutions, the ivadomed loader with
pybids
considers the last part of the filename (after the last underscore) as the modality as mentioned here. This means the two contrasts are treated as one in effect as both have the suffixMTS
.To train separately (which I assume is the goal), it looks like we would have to use different suffixes. However, this doesn't look like a clean solution and I am open to any other suggestions!