There are files called lh.area and lh.volume that you can use instead of
lh.thickness. Make sure to use the --jac flag when applying
mri_surf2surf to area or volume (but not thickness). This applies
jacobian correction to preserve the total area or volume. When you run
mri_segstats, include the
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Hi again Doug,
Sorry for not realizing this earlier, but I actually found a workflow that you
created, which outlines the steps really well.
(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness)
However, instead of 'fsaverage' I us
You can create an annotation with mris_seg2annot and then view it in
freeview. Run it with --help to get docs
On 06/14/2018 02:18 PM, Ryan Flores wrote:
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>
> Great. That seemed to have worked. Is there a way to inspect that the ROIs
> have been correctly p
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Great. That seemed to have worked. Is there a way to inspect that the ROIs have
been correctly placed? Perhaps by using freeview?
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
On 6/14/18, 11:02 AM, "freesurfer-boun...@nmr.mgh.harvard.edu
The --trgsurfval is just the output (ie, lh.atlas.nii.gz sampled onto
the surface of the subject). Use nii.gz or mgz for the output (not img).
On 06/14/2018 01:46 PM, Ryan Flores wrote:
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> Thank you for your response. Just to clarify, the first command sh
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Thank you for your response. Just to clarify, the first command should be
mri_vol2surf, correct? It appears to have worked; however, I'm not sure what my
--trgsurfval should be? I'm trying the following commands, where mni is the
subject directory fo
You can always get info by running the command with --help.
mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh
--projfrac-max 0 1 .1 --o lh.atlas.nii.gz
This assumes that the atlas is in registration with the mni152 (you can
test with tkregister --mov atlas.nii.gz --s subject --reghea
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Hello all,
I am hoping to obtain structural information (e.g., cortical thickness, surface
area, and volume) based on the n30r83 (aka Hammersmith) atlas, which is in MNI
space. The atlas differentiates between the hemispheres by using odd/even
numbe
