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 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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