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): 7829.8 Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396 Left-Inf-Lat-Vent Volume (mm3):594 Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569 Left-Cerebellum-White-Matter Volume (mm3):12668 Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203 Left-Cerebellum-Cortex Volume (mm3):44113.2 Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804 Left-Thalamus-Proper Volume (mm3):5752.8 Left-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.
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): 7829.8 Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396 Left-Inf-Lat-Vent Volume (mm3):594 Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569 Left-Cerebellum-White-Matter Volume (mm3):12668 Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203 Left-Cerebellum-Cortex Volume (mm3):44113.2 Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz):43804 Left-Thalamus-Proper Volume (mm3):5752.8 Left-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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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): 7829.8 Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396 Left-Inf-Lat-Vent Volume (mm3):594 Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569 Left-Cerebellum-White-Matter Volume (mm3):12668 Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203 Left-Cerebellum-Cortex Volume (mm3):44113.2 Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804 Left-Thalamus-Proper Volume (mm3):5752.8 Left-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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 mailto: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): 7829.8 Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396 Left-Inf-Lat-Vent Volume (mm3):594 Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569 Left-Cerebellum-White-Matter Volume (mm3):12668 Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203 Left-Cerebellum-Cortex Volume (mm3):44113.2 Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz):43804 Left-Thalamus-Proper Volume (mm3):5752.8 Left-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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- gAbE
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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): 7829.8 Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396 Left-Inf-Lat-Vent Volume (mm3):594 Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569 Left-Cerebellum-White-Matter Volume (mm3):12668 Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203 Left-Cerebellum-Cortex Volume (mm3):44113.2 Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804 Left-Thalamus-Proper Volume (mm3):5752.8 Left-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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e du/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- gAbE
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
On 4/25/17 2:50 PM, Gamaliz wrote:
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 mailto: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 <mailto: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): 7829.8 Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396 Left-Inf-Lat-Vent Volume (mm3):594 Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569 Left-Cerebellum-White-Matter Volume (mm3):12668 Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203 Left-Cerebellum-Cortex Volume (mm3):44113.2 Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz):43804 Left-Thalamus-Proper Volume (mm3):5752.8 Left-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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- gAbE _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- gAbE
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Gamaliz