Was the aseg correct in the cross? If you can upload this subject (all the cross and long timepoints) we can take a look

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Malo Gaubert Sent: Monday, May 3, 2021 10:19 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA in longitudinal processing

External Email - Use Caution Hello,

Any idea on how to correct pial & white matters segmentation splitting out on lateral ventricle while aseg is correct (see previous message below)? Thank you.

Le lun. 26 avr. 2021 à 08:38, Malo Gaubert <malogaubert@gmail.commailto:malogaubert@gmail.com> a écrit : Hello,

Any idea on how to fix these longitudinal issues?

Le jeu. 15 avr. 2021 à 09:44, Malo Gaubert <malogaubert@gmail.commailto:malogaubert@gmail.com> a écrit : Hello FreeSurfer developers,

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/LongitudinalTutorialhttps://secure-web.cisco.com/1tX5fu_Ax9KbuzA3-e77cyR3x9mZzkFLtWRrRWH3fyTUdv1WD_ki1GLxZ82DWLz_teRZ96w91IMHTeGHi2gjEZuR8iVAPBgg-swudBYPvMSn1FhP5yr5BFToH-M7L0nM8NjsUmp5kMiCY4ixrdU8PxaZtgFJlZylT0Oo9Ce6lvex-XFnKUOXKmAAoMiFNmwbX0hfUIydiJuyPMboMY2V9BdO0nA4L2NJOhjOd5BVjUtdoPv93Rk0pWvVMj-dIE-GiQbspTxio-f4qUNKym07mUQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FLongitudinalTutorial 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 (session 1 of the subject; cross-sectional), while the aseg is fine (this area is considered as Lateral ventricle, see figure 2 attached). 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=display of the norm of my norm and pial/white for the two timepoints (long)) and/or some weird/non straight lines for pial or white (see figure 3, especially between temporal pole and the rest of the brain). What could be the error in this case? Could it be related to some bad quality of T1w images?

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0.tar.gz 2) Platform: Ubuntu 18 (Virtual Machine on remote server) 3) uname -a: Linux ubuntu18-cbrain-042020 4.15.0-135-generic #139-Ubuntu SMP Mon Jan 18 17:38:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Any help would be appreciated.

Best, Malo