There are two questions here: 1. Why did it stop? Your log file does not give an indication. Is it possible it ran too long and was automatically terminated after a period of time? 2. Starting it from where it stopped. This is hard as you need to be able to see where it stopped then match that to the flags for recon-all. In some cases you can run with -make all instead of -all. This has always been a bit flaky. The easiest thing is going to be just to re-run from scratch. If a case has aseg.presurf.mgz, you can run it with -autorecon2-noaseg which will save you a lot of time.
On 3/1/2022 5:09 PM, REEM ABU BAKR BAHATHIQ wrote:
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Hello Freesurfer experts
I ran the full Recon-all pipeline on my 400 .scans data. I wanted to get the "wmparc.mgz" image of each subject. But I couldn't find it in some of them !!
Where can I find the error file for the subject, as I think the process is not completed here?
I would also like to inquire about the way to restart Recon-all from where the pre-processing stopped. How can I determine which step stopped processing and what should I write from a command in Linux to complete the processing process?
The attached picture shows the processing output for the subject that I think something went wrong with it
Thanks in advance image.png
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