Follow-up on recent processing results

[Mathilde-16]

As our cohort is not ready yet (sorry for the delay), I've launched the last version of the script on 72 sessions (12 subjects and each with 6 sessions) I've since the beginning.

I can't send you directly here the QC zip file due to its size, therefore I share you a WeTransfer link so that you can have access to the QC zip file.

According to this QC, the PMJ seems to be detected with success.
Regarding the sct_process_segmentation, I've some doubts. For example, for sub-MS03_ses-aera01 session below, it's C3-C4 which is identified (in red) instead of C2-C3 :

Here is output CSA :
csa-SC_T1w.csv

[jcohenadad]

For example, for sub-MS03_ses-aera01 session below, it's C3-C4 which is identified (in red) instead of C2-C3 :

It is important to understand that the 64mm distance from the PMJ corresponds to the C2-C3 disc in average across a population. The notion of "average" means that it is not exactly 64mm for each individual, but that there is some variation, as illustrated in Figure 3 of the Bedard et al. paper.

[Mathilde-16]

Hi @jcohenadad, thanks to the manual correction, outliers values of CSA have almost all been solved. I'll share you these new results thanks to the One Drive link as soon as possible, I haven't finished working on it yet, but soon !

But I've a trouble with the processing of the t1_ax_ce folder. I've realised that a lot of session results are missing in the CSA output file. Indeed, this file contains results of 9 sessions but the t1_ax_ce folder corresponds to 439 sessions, therefore the sct_process_segmentation command hasn't produced any results for most acquisitions, even when the segmentation and the PMJ detection have passed the QC. Then, I've looked at the log files and the error is as below :

[jcohenadad]

pls show sag view of 2-3 subjects where you see this error

[Mathilde-16]

Yes sure. I'm going to send you them by email in order to avoid letting several data here in a public repo.