It is seg faulting at the defect correction stage which is before the FLAIR would be used. At this point it should be identical to the T1-only analysis. Check your commands to make sure they are the same except for the FLAIR part

On 1/16/2020 9:55 AM, Swanson,Clayton wrote:

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Hello FreeSurfer Developers,
I am attempting to perform a recon-all using a T2-FLAIR image.  I have already run this particular participant through recon-all with their T1 image without error.  While running the recon-all using the T2 the process exited with error stating a segmentation fault. 

Is there any way to run fix this problem on my end or better understand why this would be occurring? 

I have uploaded the recon-all.log for your convenience. 

Thank you,
Clayton


________________________________
Clayton Swanson MS
Graduate Research Assistant & PhD Student
Sensorimotor Neuroimaging Laboratory
Colorado State University
Office: (970) 491-6160


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