You are almost there. You need to swap mov and targ in your tkregister2 command. I also found these instructions on how to do this, but you seemed to have figured it out already https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 4/10/19 6:38 PM, Larson, Kathleen E wrote:
External Email - Use CautionThanks. I'm now able to run the command without error. However, the surface output is not lined up with the original image that I used as the FS input. Here is the code I use:
tkregister2 --mov orig.mgz --targ rawavg.mgz --reg register.native.dat --s $subject mri_surf2surf --reg register.native.dat rawavg.mgz --hemi lh --sval-xyz pial --tval-xyz rawavg.mgz --tval ./lh.native.pial --s SUBJECT_ID
My guess is that I am somehow not creating the proper transform... do you see anything here that I should be doing differently?
Thanks, Katie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [DGREVE@mgh.harvard.edu] Sent: Monday, April 08, 2019 12:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2surf help
Have you looked at the help? Run with --help and look at example 4 doug
On 4/4/19 9:56 PM, Larson, Kathleen E wrote:
External Email - Use CautionHello FreeSurfer developers,
I'm having trouble running the command mri_surf2surf, and I haven't been able to find a fix in the message archives (a similar question has been asked, but I couldn't find the answer). I am trying to convert the pial and white matter surfaces for a series of subjects back to the anatomical space. I have computed the registration matrix to transform the surfaces, but am having trouble with the mri_surf2surf syntax. This is the command I am trying to run:
mri_surf2surf --hemi lh --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --s <subjectID>
and I get an error saying that --tval-xyz requires an input volume. (The syntax described on the website (https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr...) is out of date.) I have tried to use rawavg.mgz as the input volume, but then I get an output that can only be read as a scalar overlay, and I need an actual surface. When I try to use a surface as the input, I get an error saying that the file type cannot identified.
Do you have any suggestions for what I am doing wrong?
Thank you,
Kathleen Larson Department of Biomedical Engineering Vanderbilt University 304 Featheringill-Jacobs Hall (425)-894-2005
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