Dear All,
I was wondering whether there is a simple way to pass T1 segmentations I have from another software to Freesurfer, in order to do the remaining recon-all steps?
Thank you in advance, James
Hi James
what kind of segmentation? If gray/white you could replace the wm.mgz and go from there, otherwise you would replace the aseg.mgz. In either case, make sure you use our conventions (the FreeSurferColorLUT.txt for the aseg, or set every wm voxel to the brain.mgz intensity if it is in the white matter, and zero otherwise)
cheers Bruce On Thu, 3 Dec 2015, james pardon wrote:
Dear All, I was wondering whether there is a simple way to pass T1 segmentations I have from another software to Freesurfer, in order to do the remaining recon-all steps?
Thank you in advance, James
Dear Bruce,
I'm following your advice and now have replaced wm.mgz. Could you please let me know what options I should add to recon-all so not to overwrite my wm.mgz and get things going from this point? ( I have already run the recon-all so just need to re-run it with the replaced wm.mgz)
aseg.mgz is not a problem at all.
Thank you James
On Thu, Dec 3, 2015 at 1:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi James
what kind of segmentation? If gray/white you could replace the wm.mgz and go from there, otherwise you would replace the aseg.mgz. In either case, make sure you use our conventions (the FreeSurferColorLUT.txt for the aseg, or set every wm voxel to the brain.mgz intensity if it is in the white matter, and zero otherwise)
cheers Bruce
On Thu, 3 Dec 2015, james pardon wrote:
Dear All,
I was wondering whether there is a simple way to pass T1 segmentations I have from another software to Freesurfer, in order to do the remaining recon-all steps?
Thank you in advance, James
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.
Try recon-all -make all
On Jan 2, 2016, at 4:37 PM, james pardon james.pardon15@gmail.com wrote:
Dear Bruce,
I'm following your advice and now have replaced wm.mgz. Could you please let me know what options I should add to recon-all so not to overwrite my wm.mgz and get things going from this point? ( I have already run the recon-all so just need to re-run it with the replaced wm.mgz)
aseg.mgz is not a problem at all.
Thank you James
On Thu, Dec 3, 2015 at 1:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi James
what kind of segmentation? If gray/white you could replace the wm.mgz and go from there, otherwise you would replace the aseg.mgz. In either case, make sure you use our conventions (the FreeSurferColorLUT.txt for the aseg, or set every wm voxel to the brain.mgz intensity if it is in the white matter, and zero otherwise)
cheers Bruce
On Thu, 3 Dec 2015, james pardon wrote:
Dear All, I was wondering whether there is a simple way to pass T1 segmentations I have from another software to Freesurfer, in order to do the remaining recon-all steps?
Thank you in advance, James
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
james pardon