Hello FS experts,
I'm trying to get the volume of a binary mask on orig.mgz. I know that FS uses a more sophisitcated approach than simply counting the number of voxels within the mask and I'd like to apply the same approach. Is there any way to get the volume for a defined mask with the same approach that FS computes the volumes for aseg.mgz?
thanks. Ehsan
Hi Ehsan
we do partial volume estimation for all border voxels in a label (like your mask). Look at the help in mri_segstats and you should be able to sort it out
cheers Bruce
On Wed, 1 Nov 2017, Ehsan Tadayon wrote:
[490353fad4dbc1e2d4df113f9e07e0fb7d507be0.png?u=375924] Hello FS experts, I'm trying to get the volume of a binary mask on orig.mgz. I know that FS uses a more sophisitcated approach than simply counting the number of voxels within the mask and I'd like to apply the same approach. Is there any way to get the volume for a defined mask with the same approach that FS computes the volumes for aseg.mgz?
thanks. Ehsan
Look in the recon-all.log file for the command that generates the aseg.stats file. Use that command but change aseg.mgz to whatever your mask is (and change the output). Don't include the LUT on the command line.
On 11/1/17 10:24 PM, Ehsan Tadayon wrote:
Hello FS experts,
I'm trying to get the volume of a binary mask on orig.mgz. I know that FS uses a more sophisitcated approach than simply counting the number of voxels within the mask and I'd like to apply the same approach. Is there any way to get the volume for a defined mask with the same approach that FS computes the volumes for aseg.mgz?
thanks. Ehsan
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Thanks Bruce Thanks Doug
that was a great help. I was able to run it as you mentioned. I also tried to see if I can get the same values as aseg.stats file that you mentioned. I created a binarized mask from aseg.mgz for a structure and ran the same command. However, the values that I get are a little bit different from aseg.stats file. I used mri_segstats as you mentioned.
thanks again for your help. best, Ehsan.
On Sun, Nov 5, 2017 at 1:34 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Look in the recon-all.log file for the command that generates the aseg.stats file. Use that command but change aseg.mgz to whatever your mask is (and change the output). Don't include the LUT on the command line.
On 11/1/17 10:24 PM, Ehsan Tadayon wrote:
Hello FS experts,
I'm trying to get the volume of a binary mask on orig.mgz. I know that FS uses a more sophisitcated approach than simply counting the number of voxels within the mask and I'd like to apply the same approach. Is there any way to get the volume for a defined mask with the same approach that FS computes the volumes for aseg.mgz?
thanks. Ehsan
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The difference is probably due to the partial volume correction, which will be different with different segmentations
On 11/06/2017 03:06 PM, Ehsan Tadayon wrote:
Thanks Bruce Thanks Doug
that was a great help. I was able to run it as you mentioned. I also tried to see if I can get the same values as aseg.stats file that you mentioned. I created a binarized mask from aseg.mgz for a structure and ran the same command. However, the values that I get are a little bit different from aseg.stats file. I used mri_segstats as you mentioned.
thanks again for your help. best, Ehsan.
On Sun, Nov 5, 2017 at 1:34 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Look in the recon-all.log file for the command that generates the aseg.stats file. Use that command but change aseg.mgz to whatever your mask is (and change the output). Don't include the LUT on the command line. On 11/1/17 10:24 PM, Ehsan Tadayon wrote:Hello FS experts, I'm trying to get the volume of a binary mask on orig.mgz. I know that FS uses a more sophisitcated approach than simply counting the number of voxels within the mask and I'd like to apply the same approach. Is there any way to get the volume for a defined mask with the same approach that FS computes the volumes for aseg.mgz? thanks. Ehsan _______________________________________________ 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.
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