Re: [Freesurfer] Help importing files from a previous SPM analysis

you have to do the whole thing

On 12/21/2015 06:09 PM, Luis Fernado Silva Castro de Araújo wrote:

Do I have to run recon-all entirely in order to extract volume for a few Brodmann's areas? Or is there a way of optimizing the process by striping it of any unneeded calculations?

It is taking 21h to analyze one subject.

Best, luis

2015-12-22 9:44 GMT+11:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:

If you're doing anatomical analysis, then FSFAST is not needed
(nor its
directly structure). If you have an input anatomical volume  in any
format, then just run

recon-all -s yoursubjectname -all -i inputfile

inputfile can include img but be warned that img does not have
information about head orientation. This may cause a catastrophic
failure (eg, the head is upside down). If the head is left-right
reversed, then it probably won't fail but everything will be
left-right
reversed. don't say I did not warn you:)


On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote:
>
> Dear Douglas,
>
> It's an anatomical analysis. Perhaps I misunderstood the requirement
> for setting up the directories in the FSFAST for the recon-all
command.
>
> If that is the case, it is then a matter of converting my img files
> into mgz and run recon-all on them, am I right?
>
> Does the command recon-all also gives me volumes for specific
> Brodmann's areas? Or do I have to run a labeling to that?
>
>
> Thank you,
>
> luis
>
>
>
>
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