Hi, I have some question on mri_segstats
1) --seg-erode Nerodes Is it the size of the window for erosion?
2) --robust percent Is it the percentage of tissue in each voxel?
3) If I want to combine Left and Right together and calculate the statistics, for example the mean and std of the "Left/Right Caudate", how to do that?
Thank you, Fang
Hi Fang,
On 04/26/2013 12:35 PM, Fang CAO wrote:
Hi, I have some question on mri_segstats
- --seg-erode Nerodes
Is it the size of the window for erosion?
I'm not sure what you mean. Nerodes is the number of recursive 1 voxel erosions.
- --robust percent
Is it the percentage of tissue in each voxel?
It computes a "trimmed" mean/std in each ROI by excluding the top and bottom X% intensities.
- If I want to combine Left and Right together and calculate the
statistics, for example the mean and std of the "Left/Right Caudate", how to do that?
Create a new segmentation mask with mri_binarize --i aseg.mgz --match 11 50 --o lrcaudate.mgz then run mri_segstats --seg lrcaudate.mgz --id 1 ... doug
Thank you, Fang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thank you for the answers.
2013/4/26 Douglas N Greve greve@nmr.mgh.harvard.edu
Hi Fang,
On 04/26/2013 12:35 PM, Fang CAO wrote:
Hi, I have some question on mri_segstats
- --seg-erode Nerodes
Is it the size of the window for erosion?
I'm not sure what you mean. Nerodes is the number of recursive 1 voxel erosions.
Does it use the same algorithm as in "mri_binarize -erode Nerodes"
- --robust percent
Is it the percentage of tissue in each voxel?
It computes a "trimmed" mean/std in each ROI by excluding the top and bottom X% intensities.
Does it always exclude the X% intensities, or it uses some outlier detection algorithm to identify maximum X% outliers?
Fang
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Fang CAO