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