I tried using it both as an input and output and the produced files both seemed wrong, so I was trying different combinations.
The template (a picture of it is attached in my initial email) is a mask for primary visual areas, and to export and use it in a different software I am trying to superimpose it on top of a complete skull stripped volume file like rawavg. I am trying to reconstruct that volume file in that other software hoping to visualize&use the mask on the software's native surface file. Thank you for the help, Idil ________________________________________ From: [email protected] [[email protected]] on behalf of Douglas N Greve [[email protected]] Sent: Monday, August 14, 2017 9:36 PM To: [email protected] Subject: Re: [Freesurfer] mri_binarize/mri_mask command help mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz). can you elaborate on what you are trying to do? what do you mean by a template? On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote: > > Dear FreeSurfer experts, > > I am trying to use the following command to merge the volume file of a > template with original T1 orientation*, with a file like rawavg to get > the full brain volume, but the following attached image gets produced > and I am pretty sure, as a freesurfer novice, I am using a wrong > command line. I have tried mri_mask as well but do not think it is the > command to go. I also checked if two volumes are in the same > orientation using mri_orient. > > mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf > > * (I have the native oriented version of this volume template as well, > and I attached a photo of the template as well) > > I would deeply appreciate if someone could help me correct my command > line. Thank you all for the time and help > > Idil > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
