the latter is easier than the former. You can use mri_convert with the
-rl flag ("reslice like"). From the subject's mri dir you could do:
mri_convert -rt nearest -rl rawavg.mz aseg.mgz aseg.orig_space.mgz
or
mri_convert -rl rawavg.mgz norm.mg norm.orig_space.mgz
where -rt nearest tells mri_convert to use nearest neighbor interpolation
instead of trilinear or cubic, which it needs to do for a label map
cheers
Bruce
On Mon,
3 Apr 2017, Dhaval Shah wrote:
Hi Bruce,
Thank you for the message. My image has isotropic voxel size 1mm3. Is there
a way where i can keep the original matrix size (256x256x160) instead of
re-sampling to (256x256x256)? or is there a way where i can resample the
data to my original matrix size after i run recon-all?
Thank you.
On Mon, Apr 3, 2017 at 5:37 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Dhaval
we resample all input images to 256^3 and 1mm isootropic unless
we are
explicitly told not to. We call this "conforming"
cheers
Bruce
On Mon, 3 Apr 2017, Dhaval Shah wrote:
> Just a correction,
>
> The original image matrix size is (256x256x160) and the
resulted image
> matrix size is (256x256x256).
>
> 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
>
>
>
>
> --
> 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
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>
>
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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//http://mbl.bnac.net
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