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Dear Freesurfer experts,
I would appreciate any help regarding my previous question:
I need to transform a bunch of MNI coordinates to subject's space. I have
already registered my subjects to cvs_avg35_inMNI152 using
mri_cvs_register. How can I use
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> There is no linear transformation between the two. Vertex coordinate is
> equal to surfaceRAS when the point that you have selected is actually one
> of the vertices on the chosen surface. However, if the point is not on the
> surface, it finds the
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Hi Joel,
you need to find the corresponding voxel ( using ras2vox transformation
matrix) and then apply your vox2ras-tkr matrix to it. it would give you the
tkrRAS coordinate.
cheers,
Ehsan.
On Tue, Sep 4, 2018 at 12:40 PM Bruss, Joel E wrote:
>
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Hi,
I'm tyring to transform a bunch of MNI coordinates to subject's space using
mri_cvs_register and applyMorph. I have run the mri_cvs_register but
could'nt find detailed description of applyMorph. I appreciate any input
on what command should be
e released a 400-region parcellation, as well as other
> resolutions (100 to 1000 parcels), which map to the original 7 and 17
> networks (https://github.com/ThomasYeoLab/CBIG/tree/master/
> stable_projects/brain_parcellation/Schaefer2018_LocalGlobal).
>
> Regards,
> Thomas
>
>
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Hi,
Is there an easy way to sub-parcellate each network in Yeo-2011 (for
instance network 7) into several clusters (ROIs) for an individual subject?
thanks
Ehsan.
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ts file. Use that command but change aseg.mgz to whatever your mask
> is (and change the output). Don't include the LUT on the command line.
>
> On 11/1/17 10:24 PM, Ehsan Tadayon wrote:
>
> Hello FS experts,
>
> I'm trying to get the volume of a binary mask on orig.mgz. I know th
Hello FS experts,
I'm trying to get the volume of a binary mask on orig.mgz. I know that FS
uses a more sophisitcated approach than simply counting the number of
voxels within the mask and I'd like to apply the same approach. Is there
any way to get the volume for a defined mask with the same
e anatomical to a bounding box around
> the brain. This is a bit tricky as you also have to compute a new
> registration. I can help step you through the process if you want to go
> in that direction.
>
> On 03/22/2016 11:50 AM, Ehsan Tadayon wrote:
> > Hi Doug,
> >
> &
, Mar 16, 2016 at 11:27 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> that's going to create a pretty big volume as it will map your functional
> time course to a 256^3 float volume. If you have 100 time points, then that
> will be about 7G.
>
> On 3/16/16 3:27 PM
nds like
> you ran out of memory though
>
> Cheers
> Bruce
>
> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon <ehsan.tadayo...@gmail.com>
> wrote:
> >
> > Ehsan
>
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Dear Freesurfer experts,
I'm trying to run mri_vol2vol on a functional mri to resample it onto
orig.mgz. I get this error:
```
mri_vol2vol(98217,0xa0ce01d4) malloc: *** mach_vm_map(size=262144) failed
(error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to
Dear Freesurfer experts,
I am using Freesurfer v5.3 for recon-all. Previously, It usually took me 24
hours to complete one subject on Centos cluster. I have noticed that some
subjects are finished in less than an hour even though I have not provided
other flags like openmp or use-gpu. The log
Hello
I'm new to freesurfer, I have some .nii images that i converted to .mgz
via mri_converter in freesurfer and run recon-all on them!
it seems everything is fine and i've got stats in m subjects folders. but
when I try to do tkmedit to visualize images it gives me an error:
Tkmedit couldn't
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