External Email - Use Caution what do you mean that you won't want to do any resampling? How else would you apply a transform? Or do you mean that you want to use nearest neighbor resampling (so no interpolation)? If so, you can use mri_vol2vol with the --interp nearest option
On 5/3/2023 4:21 PM, Wighton, Paul wrote: > External Email - Use Caution > > Hi Daniel, > > It's been a while since I looked into this, but I think you'll need to use > `lta_convert` to convert your lta to xfm format, then use > `mri_add_xform_to_header` to overwrite the header of your phase map. > > You might have to extract the current transform from your phase map, apply > the robust_regsiter transformation then write the resulting xfm back to your > phase map file. > > There is also mri_convert which has an `--apply_transform` flag, but I think > that resamples the data. > > -Paul > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Balentine, Daniel Grimm > <dbalent...@mgh.harvard.edu> > Sent: Wednesday, May 3, 2023 4:06 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] apply an existing linear transform to a GRE phase map > > External Email - Use Caution > Hello FreeSurfer Developers, > > I hope you are well. I’m attempting to apply an .lta file generated by > mri_robust register. The files I want to apply the transform on are GRE phase > maps, so I don’t want to do any resampling. > > I was looking around mri_vol2vol, but all the examples seem to involve > resampling to a target scan. How would I go about this if I simple want to > apply this linear transform on the phase maps (nii) in freesurfer? > > > 1. Freesurfer version 7.3.0 > 2. Platform: CentOS Version 7 > > Sincerely, > > Daniel Balentine > > Data Analyst > Athinoula A Martinos Center for Biomedical Imaging > Massachusetts General Hospital > 149 - 13th Street > Charlestown, MA 02129 > dbalent...@mgh.harvard.edu > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1vyO6jpX8iajK-1t5rnT-drlZOlAx8DRC0xteWXDnkEHJiWYO7S5gT-OZtgWRwFOiini7NuVel0DV3Cf9w7S5cSjcRBPKfY1YbmpcnowQsB01yOQuCSSLllBUZ71B3-o0gqqGIKNJhwg4OJoFQjwDgZMkMyA_2_E_w-DvnTToMV9MpKF-QKgU8wwuddUhI4dQ6UQAMA6pAx3FpalKeLhTMN9K-iHpdeEfl2m80bYnLGE1yFkqPpAvHe_07PvZWNyL_Q4KYPMKfHmlZCY_WN9kKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
