Hello Everyone,
I've run the Freesurfer 6.0 and created the sub-brainstem structures (e.g.,
pons, midbrain, etc.). I would like to convert the
brainstemSsLabels.v10.mgz results to a .nii file. However, unlike when I
use mri_convert for aseg.mgz, I only get an image of the brainstem itself
as a sin
Hello,
Is the AtlasMesh under the following pathway a standard mesh structure? If
so, what is it? Better yet, is there a way for those meshes in the
AtlasMesh to be converted to a standard stl file or some other standard
mesh file format? To be clear, I know the .gz is a compressed file; I'm
refe
That was the issue. Thank you!
Best,
Jonathan Plasencia
Graduate Student
NSF Graduate Research Fellow
*School of Biological and Health Systems Engineering*
*Arizona State University*
Email: jplas...@asu.edu
Phone: (480)861-7017
On Fri, Oct 23, 2015 at 8:17 AM, wrote:
>
> My guess is th
Hello,
I'm trying to segment the brainstem into subparts. I found online for
freesurfer 5.3 you can use the following link to install the need codes:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
which was from the following freesurfer question/solution:
http://www.mail-archive.co
fis...@nmr.mgh.harvard.edu
Best,
Jon
On Mon, Aug 3, 2015 at 1:18 PM, Bruce Fischl
wrote:
> and you are saying that aseg.nii does *not* match the voxel counts in
> aseg.mgz? That is surprising. Can you email me the aseg.mgz?
>
>
> On Mon, 3 Aug 2015, Jonathan Plasencia wrote:
>
> I've g
i, Jul 31, 2015 at 2:31 PM, Jonathan Plasencia
wrote:
> Ok, I will give this a look. Thank you everyone.
> Best,
>
> Jon
>
>
>> cheers
>> Bruce
>>
>> On Fri, 31 Jul 2015, Jonathan Plasencia wrote:
>>
>> This is what we did from terminal:
>&g
Ok, I will give this a look. Thank you everyone.
Best,
Jon
> cheers
> Bruce
>
> On Fri, 31 Jul 2015, Jonathan Plasencia wrote:
>
> This is what we did from terminal:
>>
>> mri_convert aseg.mgz aseg.nii --out_orientation RAS
>> mri_convert aseg.mgz a
, 0, 0)*
*j_ras = (0, 0, -1)*
*k_ras = (0, 1, 0)*
*Setting output orientation to RAS*
*Reslicing using trilinear interpolation *
*writing to aseg.nii...*
*** I ran this command from within the subject's mri folder.*
Should we try this without * --out_orientation RAS **?*
Best,
Jonathan Plas
We are using the following line:
mri_convert aseg.mgz aseg.nii --out_orientation RAS
Best,
Jonathan Plasencia
Graduate Student
NSF Graduate Research Fellow
*School of Biological and Health Systems Engineering*
*Arizona State University*
Email: jplas...@asu.edu
Phone: (480)861-7017
On Fri
I've converted the aseg.mgz file to .nii (need data in nii to do some
further work on the data). However, the number of voxels for a given
structure changes when comparing the stats file (from freesurfer) to the
created .nii file. What is happening here? Is there a fix for this? I would
expect the
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