On 10/21/2021 6:59 AM, Wacker, Ewa Helene wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

for my project I am using Freesurfer 7.1 to examine the hippocampal volumes of patients with major depressive disorder (and controls) using the automatic segmentation. Therefore I have ran recon-all on all the 242 subjects. 12 of them did exit with an ERROR in form of a hard failure. I had troubles finding enough information online on how I could try to fix them by myself.

The reports state the following:

• for 2 subjects" 3d Normalization pass: could not read source volume brain.mgz\00"  - /example is subject AIDAB_2017_T1/

/Not sure what is going on here. This one had an mri_watershed failure on the first run. Look at the T1.mgz volume and see if something looks wrong/

• for 9 "could not find enough control points" /example is subject AIDAB_3097_T1/

This one looks like it failed in the first normalization stage. Look at nu.mgz

• for 1 "MRI_watershed Error: global Region of the brain empty" /example is subject AIDAB_4007_T1/

/This is the same as the first one/

Is there any chance that there will be a way to include some of the subjects? If needed, I would be happy to send more recon-all.log files, I attached one of each group to this email.

Thank you for your time and support,

Best regards,

Ewa Helene Wacker

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