External Email - Use Caution Thanks. 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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [dgr...@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 Caution > > Hello 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.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat&data=02%7C01%7Ckathleen.e.larson%40vanderbilt.edu%7Cba17f3d3fc0c4afcfd3a08d6bc479a23%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636903413085822718&sdata=YnDMci9yiERFJr7aODvHk7b91e7cLbUxBRO1agMZAH8%3D&reserved=0) > 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 out of date.)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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Ckathleen.e.larson%40vanderbilt.edu%7Cba17f3d3fc0c4afcfd3a08d6bc479a23%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636903413085822718&sdata=9h3EeskXFr95oJSlYxSWdFmu3RMPo8MEMVMGVTxmW%2FA%3D&reserved=0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Ckathleen.e.larson%40vanderbilt.edu%7Cba17f3d3fc0c4afcfd3a08d6bc479a23%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636903413085832722&sdata=gkL4wO5S4uX%2BO8ZoKY25bn%2BLIkaw7NBdZN%2B1J9AiQVs%3D&reserved=0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
