Dear Dhaval,
when your recon-all finishs the process you will get images 256^3 and 1mm
isootropic.
The you can simply follow the instructions mentioned here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to send your
images back to native space.
All the best,
John
>
> On Mon, Apr 3, 2017 at 4:35 PM, Dhaval Shah <ds...@bnac.net> wrote:
> Hi All,
>
> I am new and a very basic question about freesurfer processing.
>
> I ran recon-all on a high res-T1 image(128x128x80 matrix size), but
> after recon-all the folder mri contains resulted (brain.mgz and
> orig.mgz) T1 images has (127x128x128 matrix size).
>
> 1) how come the dimensions are changed? Is it normal?
> 2) how can i keep the dimensions same as the original?
> 3) is it possible that i will always get the higher matrix size image
> data?
>
> for simplicity, i converted resulted orig.mgz to nii format and loaded
> it in to fslview. Please find the first image (Original) and the
> second image (after recon-all but orig.mgz).
>
> Your help is greatly appreciated.
>
> --
> Kind regards,
> Dhaval Shah
>
> MRI Research fellow,MRI Physicist,Clinical Trial Research Staff
> Buffalo Neuroimaging Analysis Center
> State University of New York at Buffalo
> Department of Neurology
> 100 High St., D-2, Buffalo, NY 14203
> [MailScanner has detected a possible fraud attempt from "ds...@bnac.net"
> claiming to be MailScanner has detected a possible fraud attempt from
> "ds...@bnac.net" claiming to be
> ds...@bnac.net//http://mbl.bnac.net](http://ds...@bnac.net/http:/mbl.bnac.net)
>
>
>
>
> --
> Kind regards,
> Dhaval Shah
>
> MRI Research fellow,MRI Physicist,Clinical Trial Research Staff
> Buffalo Neuroimaging Analysis Center
> State University of New York at Buffalo
> Department of Neurology
> 100 High St., D-2, Buffalo, NY 14203
> [MailScanner has detected a possible fraud attempt from "ds...@bnac.net"
> claiming to be MailScanner has detected a possible fraud attempt from
> "ds...@bnac.net" claiming to be
> ds...@bnac.net//http://mbl.bnac.net](http://ds...@bnac.net/http:/mbl.bnac.net)
>
>
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--
Kind regards,
Dhaval Shah
MRI Research fellow,MRI Physicist,Clinical Trial Research Staff
Buffalo Neuroimaging Analysis Center
State University of New York at Buffalo
Department of Neurology
100 High St., D-2, Buffalo, NY 14203
ds...@bnac.net
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