Hello, I am currently performing a brain parcellation for a subsample of subjects within the release 2. I have noticed that the ribbon files (that I need) for some of the subjects, more specifically sub-CC00618XX16 ses-193600_desc_ribbon_space-T2w_dseg.nii.gz and sub-CC00136AN13 ses-64201_desc_ribbon_space-T2w_dseg.nii.gz are missing. (We tried to re-download the two subjects in case I was being silly but this seems to be the issue of the original database.)
Could you advice me on a way to retrieve these files?
Thanks in advance for your help.
Best,
Andrea
The ribbon files are only generated for subjects/sessions where a T1w scan was acquired. As a T1w scan was not acquired for the two sessions you are inquiring about, there are no ribbon files.
Hello. Thanks for the feedback. We suspected that there was a link with the T1w images, also missing for these sessions. Nevertheless, I don’t understand how the surfaces (.gii files for wm, pial…) could have been generated without this ribbon file? Thanks! Jessica
Hello Logan,
thank you very much for your reply.
I am not sure it helps our cause but it certainly explains it
I had a look into your structural pipeline’s github /create-myelin-map.sh and indeed the ribbons are created only if the T1w scans exist - even though the T1ws are not required for the creation of the ribbon file itself - is this correct?
If yes, I will try to follow your script to generate them if possible (as we need them to run some comparisons).
Do you think it would be good to get the ribbon creation outside the loop checking for the T1w in the future? I understand you are generating it mainly for the myelin map creation but the ribbons might be useful for other things as well.
Apologies, my last message wasn’t very clear at all. I have had a look at the scripts again, and it looks like the ribbon file is only copied to the output directory i.e. /derivatives/{subject ID}/{session ID}/anat folder if the subject has a T1w scan. So, the ribbon file is created for all subjects, but its movement into the output directory depends on the presence of a T1w image. I am not sure why the script was developed in this manner, but I am checking if there are internal copies of these files for those subjects without a T1w.
Apologies for such a delayed response. No luck in finding the ribbon files for those two subjects unfortunately… Hopefully with release 3, there will be more subjects for you to work with? I am also just about to respond to @JDubois’ post about differences in release 2 vs release 3 surfaces.
Luckily, I have managed to regenerate the ribbons myself following the dhcp scripts on github. The files serve OK at this stage for our preliminary evaluations. But we are indeed hoping to be able to move to the release 3 sooner than later.
Many thanks for your comprehensive response to the release 2 vs 3 thread
Best,
Andrea
