I am trying to apply longitudinal processing on T1w MRI data for two timepoints (~8 months between the two TP) in adolescents in order to perform vertex-based analyses.

I am following the online tutorial here for the preprocessing: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial

Thus I launched the creation of BASE followed by the LONGITUDINAL. Everything went well for recon-all for these 3 steps.

Now, I want to do the QA on the data and I have two questions regarding this QA:

1/ For one subject, for the two timepoints, the white and pial surface are entering in the left lateral ventricle as displayed in figure 1 below (session 1 of the subject; cross-sectional), while the aseg is fine (this area is considered as Lateral ventricle, see figure 2, see below).

What correction could I apply for this case ?

2/ For some subjects, there is a small shift between the pial of the two sessions (or the white; see figure 3 (see below)=display of the norm of my norm and pial/white for the two timepoints (long)) and/or some weird/non straight/zigzag lines for pial or white (see figure 3, especially between temporal pole and the rest of the brain). What could be the problem in this case? Could it be related to some bad quality of T1w images?

Any help would be appreciated.

Best regards,
Malo

Link to figure 1: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://syncandshare.lrz.de/getlink/firX4m94zEkMQG17AR9vpEm/figure_1_cross_pial-white.PNG

Link to figure2: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://syncandshare.lrz.de/getlink/fiFdfAfGsWA3Mtk7eHPiLiPE/figure_2_cross_aseg.PNG 

Link to figure3: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://syncandshare.lrz.de/getlink/fiQ3nGkLbtSdBEZLLsvmmgqg/figure_3_longitudinal.PNG