My binary mask was originally made in native space so when I transformed it
into freesurfer (conformed) space, it must have interpolated the edge of the
mask to produce values between 0 and 1. Thank yo so much for clearing that up.
Eunice
On Jan 12, 2015, at 1:49 PM, Douglas N Greve wrote:
>
The problem is that your mask is not a mask. A mask should have binary
values (ie, either 0 or 1). Yours has values in-between. mri_segstats
sets the threshold to 0.5 which gives 26526 voxels. FSL is probably
using a threshold very close to 0.
doug
On 01/12/2015 04:25 PM, Eunice Yang wrote:
Hi Doug- I uploaded an example mask. According to fslstats it has 29016 voxels
whereas mri_segstats suggests it has 26182 voxels.
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=6sthhn0ld2p
Thanks!
Eunice
On Jan 12, 2015, at 8:19 AM, Douglas N Greve wrote:
>
> Can you send mask_registered.nii.gz
Can you send mask_registered.nii.gz through our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 01/09/2015 08:58 PM, Eunice Yang wrote:
> Hello- I am trying to compute the proportion of different tissue types within
> an ROI using a mask:
> mri_segstats --seg aseg.auto.mgz --mask mask
Hello- I am trying to compute the proportion of different tissue types within
an ROI using a mask:
mri_segstats --seg aseg.auto.mgz --mask mask_registered.nii.gz --sum results
While mri_segstats is running, the terminal will show:
"There were 26526 voxels in the original mask
Voxel Volume is 1 mm
