do the commands on this link get you where you need to be? https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 08/14/2017 03:04 PM, Yagmur Ozdemir 19 wrote: > 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: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, August 14, 2017 9:36 PM > To: freesurfer@nmr.mgh.harvard.edu > 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 >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > 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 > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
