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?
On 3/29/18 4:06 PM, Anna Daniels wrote:
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 2018Attached 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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