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Dear Haley,
The Matlab version of SynthSeg writes nifty files. You could run the FreeSurfer
command to convert to mgz (and rename to aseg, along the way):
mri_convert synthseg.nii.gz aseg.mgz
Now: I don’t know if it’s possible to simply replace FreeS
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It looks like you are transforming it to fsaverage space before
computing the statistics. If this is correct, then that will explain the
differences as that transform will involve some interpolation which will
change the values. But they should be ver
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Sorry, I don't have your previous email so I don't know what the context
is. Can you resend this email with the previous exchanges included at
the bottom? Also, please remember to send to the FS list instead of us
personally.
thanks!
doug
On 8/24/2
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You can try
mri_binarize --i aseg.mgz --csf --o csf.mgz
to get a binary map
Note that the aseg does not have sulcal CSF labeled. But you can get
that with something like
samseg --i orig.mgz --o samseg
Then run mri_binarize on the seg.mgz file
On 8/2
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Sorry for sending to the wrong place, will do in the future. Here it is.
Thanks for the suggestion! The two fov indeed don't align in freeview. I played
a little with the --no-resample option but did not acheive what I wanted.
Here I simplified the p
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Very interesting. Thanks.
On Mon, Aug 28, 2023 at 2:52 PM Douglas N. Greve
wrote:
> External Email - Use Caution
>
> You can try
> mri_binarize --i aseg.mgz --csf --o csf.mgz
> to get a binary map
> Note that the aseg does not have sulcal CS
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To confirm, the two volumes *without any transformation (ie,
"untouched")* do not align in FV but they do align in fslview? In other
words, they align in voxel space but not in RAS space?
To just copy the geometry, run
mri_convert run2.nii.gz --in_lik
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Hello Freesurfer developers,
I want to create a ROI in fsaverage space including only certain regions of the
cerebellum cortex.
Is it possible to use/extract the labels from the "# Cerebellar parcellation
labels from SUIT" or
"# Cerebellar lobule par
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Exactly, the two runs align in voxel space but not in RAS space.
mri_convert with the --in_like did the trick, thank you very much.
Now I have another scenario where the two runs also don’t align in RAS space
but where they would align in voxel space