Dear Freesurfer developers,

I am currently conducting a research project in which I am running 7T MP2RAGE images in Freesurfer version 6.0.1 but have a run into an issue.

For 3 images I receive a watershed error stating “mri_watershed error: GLOBAL region of the brain empty!” which I tried to fix using the -skullstrip -no-wsgcaatlas flag but get different results: 1 image was successful but for 2 images I get mri_watershed Error: read failed (see attachment). It appears that the last file created is the  001.mgz file hence there is no T1.mgz file created and Freesurfer therefore gives this error. I wanted to know if there is way to fix this as I have not been able to find a successful solution from the archive. I have also run the same dataset in Freesurfer version 7.2.0 and receive the same error for some scans.

 

Any help would be appreciated.

Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
uname -a: Linux pc8-009.ion.ucl.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Mar 21 12:19:18 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux

Thank you,
Kirsten