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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 <malogaub...@gmail.com> a écrit : > Hello, > > Any idea on how to fix these longitudinal issues? > > > > Le jeu. 15 avr. 2021 à 09:44, Malo Gaubert <malogaub...@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: >> https://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 >> >
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