Hi Gio,
just a wild guess... Was the temporal lobe cut off after skull stripping? In my experience there are quite a few failures in skull stripping with high resolution data, especially better than 0.7mm.
Potential workarounds:
· Run recon-all without hires flag for autorecon1. Upsample the brainmask.mgz to native resolution and use it to mask the T1.mgz of your hires data.
· I use SPM for bias field correction currently and create a brainmask from the segmentations created in that process. Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Giovana dos Santos Cover Gesendet: Donnerstag, 11. Januar 2018 17:44 An: Freesurfer@nmr.mgh.harvard.edu Cc: Reza Farivar-Mohseni, Dr Betreff: [Freesurfer] Recon-all Hires Segmentation Failure
Dear Freesurfer Developers,
I am trying to segment the grey matter and pial surface using the FreeSurfer command recon-all with the hires flag. But even though there is no error while executing my code, when I analyze the output surfaces, the segmentation is missing some areas in the brain (I attached an image to show these brain regions).
My command is:
recon-all -all -s $SUBJ -hires -i $IMAGE -expert $EXPERT_FILE
My expert file contains:
mri_em_register -p .5 mris_fix_topology -s 50 mris_inflate -n 100
Does anyone have any thoughts on how to troubleshoot my problem?
Thanks in advance,
Gio.
1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2. u-name -a: Linux ubuntu 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux [cid:image001.png@01D38B81.D9F88020]
