Hi Michele,

you should be able to do:

recon-all -i <single slice in dicom series> -s <subject id you pick> -all

you could also give it the NIFTI volume. Note that you only need to give it *one* dicom slice and it will figure out the other ones that are in the series (although of course it has to be from the right series - the anatomical).

There are pretty good tutorials on our wiki that walk you through this whole process. Check them out and see if they help cheers Bruce

On Fri, 25 Jun 2010, Michele Placci wrote:

Hi all FreeSurfer Experts, I'm a young researcher, PhD student of the University of Padua with a degree in Mathematics. I'm trying to use FreeSurfer for analyze a 3D image MRI, DICOM format (I have NIFTI too) to calculate brain volume.

I downloaded the software from your site following the instructions for a Linux CentOS 4.

Now my questions are: I have a classical MRI 3D image file, how do I send the files to FreeSurfer?

What are the instructions that I have to write in the bash? Is there a GUI to calculate brain volume?

Any help is appreciated, Thanks!

Michele.