Thanks Bruce. Following that, to convert the rth.mgz back to native space I think I can use the following command: mri_convert -rl orig/001.mgz -rt nearest rth.mgz rth.nii

thanks Mehul

On Sun, Apr 11, 2010 at 1:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Mehul, try mri_binarize instead. It would be something like:

mri_binarize --match 49 --i aseg.mgz --o rth.mgz

where 49 is the index for right thalamus proper (from the FreeSurferColorLUT.txt file) and rth.mgz is the output volume

cheers, Bruce

On Sun, 11 Apr 2010, Mehul Sampat wrote:

Hi Folks,

...

I would like to create a binary mask volume for the Right-Thalamus (all voxels of right-thalamus as 1 and 0 otherwise).

I looked at this help page http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2roi and i think I should use the following command described on this page:

mri_vol2roi --label your.label --srcvol f --srcreg register.dat --finalmskvol labelbinmask --roiavg /tmp/not.wanted.dat

is this correct ? also could someone give me an example? i am not sure what all of the parameters are. thanks Mehul

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you can also use mri_vol2vol with --regheader.

Bruce Fischl wrote:

yes, that sounds right Bruce On Sun, 11 Apr 2010, Mehul Sampat wrote:

...

Thanks Bruce. Following that, to convert the rth.mgz back to native space I think I can use the following command: mri_convert -rl orig/001.mgz -rt nearest rth.mgz rth.nii

thanks Mehul

On Sun, Apr 11, 2010 at 1:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

...

Hi Mehul, try mri_binarize instead. It would be something like:

mri_binarize --match 49 --i aseg.mgz --o rth.mgz

where 49 is the index for right thalamus proper (from the FreeSurferColorLUT.txt file) and rth.mgz is the output volume

cheers, Bruce

On Sun, 11 Apr 2010, Mehul Sampat wrote:

Hi Folks,

...

I would like to create a binary mask volume for the Right-Thalamus (all voxels of right-thalamus as 1 and 0 otherwise).

I looked at this help page http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2roi and i think I should use the following command described on this page:

mri_vol2roi --label your.label --srcvol f --srcreg register.dat --finalmskvol labelbinmask --roiavg /tmp/not.wanted.dat

is this correct ? also could someone give me an example? i am not sure what all of the parameters are. thanks Mehul

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.

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