I am still learning various aspects of Freesurfer, so pardon my questions. I am trying to run recon-all on a mnc file. It is in a folder such as /Sample1/subjects/t1/t1xxxx.mnc. 

I am pointing my SUBJECTS_DIR to /Sample1/subjects. 

But when I run recon-all -s t1, I get and error - ERROR: nothing to do. Should I be storing the .mnc file in a different location?

So it looks like it is not finding the .mnc file or can Freesurfer not process a .mnc file and I have to convert it to another format like .dcm? Also, if I am able to run recon-all, what output should I analyze to determine the gyrification index?

Thanks in advance for any pointers.

Ankita

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