Great! Thank you for the prompt response and the pointers. I am going through the tutorials now to learn how to use freesurfer and will try out what you suggested.

Thanks!
Ankita

On Mon, Jan 18, 2016 at 2:26 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Ankita

dicom is perfect. Just give recon-all a single file from the correct dicom
series and it will figure out the rest of them
Bruce
On Mon, 18 Jan 2016, Arindam Chatterjee wrote:

>
> Hi Bruce,
> Thank you for your prompt response! Sorry for my novice questions - does
> T1-weighted scan with voxels have to be in a specific format like jpg, dicom
> or mesh format?
> Ankita
>
> On Mon, Jan 18, 2016 at 1:59 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> wrote:
>       Hi Ankita
>
>       sure, we compute GI. You need to get a good T1-weighted scan
>       with voxels
>       that are about 1mm isotropic, then run it through our recon-all
>       script
>
>       cheers
>       Bruce
>       On
>       Mon, 18 Jan 2016, Arindam Chatterjee wrote:
>
>       > Hello,I am a new user of the freesurfer platform. I am a high
>       school junior
>       > conducting research on brain MRI scans and came across this
>       wonderful
>       > platform. However I am not very sure how to proceed with my
>       research - I am
>       > trying to find the whole brain Gyrification Index, which I did
>       manually on a
>       > different software called ImageJ using multiple image scans of
>       brain slices.
>       > Will freesurfer be able to analyze brain scan images and
>       provide a whole
>       > brain GI or does it only analyse and provide local GI which is
>       what I found
>       > through some forums? If so, are there any tutorials to learn
>       how to do that?
>       > Do I need any other software like MatLab to find out the
>       Gyrification Index?
>       >
>       > Thank you in advance!
>       > Ankita
>       >
>       >
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