freesurfer volumes to ITK-SNAP

[Zach]

Hi,

I'm trying to load a FreeSurfer ROI into ITK to view and edit it. I have been converting the FreeSurfer aseg.mgz to aseg.nii.mgz and loading it into ITK (using norm.nii.gz as the main image file, and aseg.nii.gz as the segmentation file). When I do this I noticed that the voxel count and volume for the ROI is different in ITK's volume and statistics than it is in FreeSurfer's stats output. The reported volume is larger in ITK. Does anyone know why this is, and how to get these numbers to agree? 

Zach

[Paul Yushkevich]

That's quite odd. Can you send an example file?

Thanks!

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[Zach]

Thanks for your response. I actually think I figured it out - seems that the aseg.stats file output from FreeSurfer takes into account "partial voluming" of voxels when calculating volume, and counts labels with a threshold partial volume. (see https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats). When I convert the aseg.mgz file into aseg.nii.gz and load it into ITK-SNAP, all partial labelled voxels are counted and results in a higher volume. This is also the case when re-calculating the ROI volume using FreeSurfer's own segmentation computation tool mri_segstats (unless you take into account partial voluming using --pv flag). I think this accounts for the difference. FYI to those doing something similar. 

On Thursday, August 25, 2016 at 2:50:18 PM UTC-7, Paul Yushkevich wrote:

That's quite odd. Can you send an example file?

Thanks!

On Thu, Aug 25, 2016 at 5:43 PM, Zach <zach...@gmail.com> wrote:

Hi,

I'm trying to load a FreeSurfer ROI into ITK to view and edit it. I have been converting the FreeSurfer aseg.mgz to aseg.nii.mgz and loading it into ITK (using norm.nii.gz as the main image file, and aseg.nii.gz as the segmentation file). When I do this I noticed that the voxel count and volume for the ROI is different in ITK's volume and statistics than it is in FreeSurfer's stats output. The reported volume is larger in ITK. Does anyone know why this is, and how to get these numbers to agree? 

Zach

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