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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