try using the switch: mri_convert -rt nearest ...
to use nearest neighbor interpolation (which is what you need to resample a segmentation volume)
cheers Bruce On Sun, 6 Jan 2019, Nillo, Ryan Michael R wrote:
External Email - Use Caution Thanks for your help, Bruce. This worked like a charm! How would I register the output segmentation back to the subject's T1.mgz? When I use mri_convert, the ROIs have a weird border around them. thanks again, Ryan ______________________________________________________________________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Wednesday, December 19, 2018 11:43:03 AM To: Freesurfer support list Subject: Re: [Freesurfer] Setting the origin in native space Hi Ryan I think mri_convert -at <tal xform> <input vol> <output vol> should do the trick. cheers Bruce On Wed, 19 Dec 2018, Nillo, Ryan Michael R wrote: > External Email - Use Caution > > Hello FreeSurfer users, > > I want to use the suit software to segment the cerebellum, however the software requires the origin be set at the anterior composure. I know the Talairach image’s origin is set at the anterior commisure and that there is a Talairach transformation in mri/transforms. Is there a way to use this information to set the origin to the anterior commisure in the native space image? > > Thanks in advance, > Ryan Nillo > Staff Research Associate > UCSF Department of Radiology and Biomedical Imaging > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives.. A searchable archive which of messages PRIOR to March 2004 is at this site A searchable archive which includes messages AFTER March 2004 is at this site. Using Freesurfer > > >
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