The missing/extra are due to sub-1mm estimation. They do not
exist independently. If you want to avoid partially volumed
voxels, you can erode the segmentation to remove border voxels
For example.I register another image to the aseg+aparc file and do some pixel-by-pixel calculations; reading the regions from the aseg+aparc and matching them on the registered file (in this case a DTI) ie: every pixel with value 2 in aseg+aparc belongs to the Left-Cerebral-White-Matter region.
however, as the aseg+aparc is missing some pixels (or have extra ones) depending on how the pixel count differs from the volume (as reported in the aseg.stats file), I will have either missing (extra) pixels.
Maybe I am asking too much? :/
On Tue, Apr 25, 2017 at 2:45 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
______________________________more exact than what?
On 4/25/17 2:07 PM, Gamaliz wrote:
Is there any way to generate a file which is more exact? Or perhaps, is that file already there?
On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
______________________________The aseg.stats is generated with partial volume estimation
On 4/25/17 12:40 PM, Gamaliz wrote:
I wrote an algorithm which uses the number of pixels per region in the aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number of pixels to match very closely the value of the volume; as each pixel represents a 1 mm3 cube.(I did the same for cortical volume and got a similar result, with an even larger discrepancy).
The aseg.stats file lists the nVoxel value, and it is basically the volume rounded up.here are some sample values for subcortical regions:
Left-Lateral-Ventricle Volume (mm3): 7829.8Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396Left-Inf-Lat-Vent Volume (mm3):594Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569Left-Cerebellum-White-Matter Volume (mm3):12668 Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz): 12203Left-Cerebellum-Cortex Volume (mm3):44113.2Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804Left-Thalamus-Proper Volume (mm3):5752.8Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz): 5899
Pretty much the values are close to the volume, but different enough to be significant. I wonder why this discrepancy.
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