Thank you so much Bruce. Looks like that worked. It has started processing the .mnc file and a lot of output is being generated. Can you also share some pointers on what stats or outputs I need to analyze to figure out the Gyrification Index?

Thank you again! Ankita

On Sat, Jan 23, 2016 at 6:27 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Ankita

you need to give recon-all a directive like -all. Also, give it the minc file as input with -i /Sample1/subjects/t1/t1xxxx.mnc

cheers Bruce On Sun, 24 Jan 2016, Arindam Chatterjee wrote:

...

Hello Freesurfer experts,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

Arindam Chatterjee(515) 419-7384 www.linkedin.com/in/chatterjeea

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