It looks like brainmask.mgz might have been corrupted. Can you run mri_info on it? Does its size look about right? Can you create brainmask.mgz again?

Dear FreeSurfer team,

after editing the brainmask.mgz (manually or with gcut), brain.finalsurfs.manedit.mgz and/or adding control points, recon-all was rerun in a loop for several subjects with the respective options 

-autorecon-pial (1) or 

-autorecon2 -autorecon3 (2), 

which resulted in the following error for only some of the subjects (while others worked fine):

(1) #@# Mask BFS Mo 19. Mär 02:35:22 CET 2018

/scratch/annadan1111/MABT1T2/reruncrosstest_pial/23358_T1_fs_edit/mri

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

threshold mask volume at 5

mghRead(/scratch/annadan1111/MABT1T2/reruncrosstest_pial/23358_T1_fs_edit/mri/brainmask.mgz, -1): read error

mri_mask.bin: could not read mask volume brainmask.mgz

Linux node011 2.6.32-696.18.7.el6.x86_64 #1 SMP Wed Jan 3 19:31:16 CST 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 23358_T1_fs_edit exited with ERRORS at Mo 19. Mär 02:35:23 CET 2018

(2) 3d normalization pass 1 of 2

white matter peak found at 110

Cannot allocate memory

Linux node098 2.6.32-696.20.1.el6.x86_64 #1 SMP Thu Jan 25 08:47:49 CST 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 44538_T1_fs_edit exited with ERRORS at Do 29. Mär 01:28:15 CEST 2018

Attached are the respective recon-all.log files in case they may be helpful. We also could not detect any similar post in the mailing list.

FreeSurfer version 6.0.0

Thank you and Happy Easter greetings from Berlin,

Anna

 

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