I actually can not remember how I got this specific output, I just sent it because of lack of info in the recon-all file. However, it stems from a problem I am encountering where I use a script to edit wm.mgz based on changes I make to filled.mgz. recon-all will fail at the same spot every time. I was able to fix the problem by running "mri_convert --in_like" on the wm.mgz using the original wm.mgz as the header reference. Attached is the recon-all.log for the failed recon-all. The puzzling thing is if I run mri_head on wm.mgz before and after mri_convert both have identical header information. I have attached the images. wm1.mgz is the output from my script and wm2.mgz is from mri_convert. Are you able to understand the difference in the files?

On Wed, Jan 8, 2025 at 8:01 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

I can't see anything wrong either. Does it happen repeatedly? Can you try running it without the -parallel flag?

On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote:
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You are correct. Attached is the correct one
On Tue, Jan 7, 2025 at 8:08 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Are you sure this is the right recon-all.log file? At the end it says it finished without error

On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote:
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Hell All,

I am testing recon-all and found that it returned with an error. I am not sure where the error is. The recon-all log file looks fine. I was testing a situation where we edit the wm.mgz and filled.mgz at the same time then run recon-all with -autorecon-wm. Attached is the recon-all log file. It should have all relevant info of version and description of our system. Any help would be appreciated.

Thank you
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