just give recon-all a single slice from the series with -i <slice file
name>.  It will figure out

the rest of them

On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote:

> Hi,
> I am a little confused about how should I save my files to execute recon-all on
> them. I have 240 slices of dicom format and I put them in a folder in my
> subjects_dir. but I get errors when using recon-all on the folder containing the
> MRIs. Can you help me with that? I really appreciate your help
>
> Thank you
>
> Dorsa
>
> On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>       Hi Dorsa
>
>       what specific models do you need? The 10-20 hours is to process the
>       data
>       from a single subject at a single timepoint. If you check out our
>       wiki
>       (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of
>       tutorials and
>       sample datasets and such
>
>       cheers
>       Bruce
>
>       On Mon, 27 Jun 2016, Dorsa Haji
>       Ghaffari wrote:
>
>       > Hi,
>       > I am graduate student at the University of Michigan and I am
>       performing
>       > research on deep brain stimulation. I want to warp an anatomical
>       brain atlas
>       > to individual patient MRIs to get the patient specific brain models
>       out of
>       > it. I chose FreeSurfer to do this and I have installed it on my
>       computer. I
>       > realized that it takes 10-20 hrs to reconstruct the image. I wanted
>       to ask
>       > if that is the time for one image? or the whole series of images?
>       > I also wanted to ask if there is a step by step tutorial on how to
>       do this.
>       >
>       > Thank you
>       >
>       > Dorsa Ghaffari
>       >
>       >
>       >
>       >
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