So do you still have an issue that needs to be solved? Can't quite tell from your email. I've fixed the webpage to add a template volume in the mri_surf2surf command, thanks for pointing out.
On 4/16/19 3:15 PM, Larson, Kathleen E wrote: > External Email - Use Caution > > Thank you! Yes, I was able to figure it out. However, even when I swap the > moving/target inputs, the surface is still not in the correct anatomical > space. > > Also, just so you are aware, the instructions on the website you gave me > aren't up to date... the --tval-xyz requires a volume input, but the > instructions don't include one, so it you run it exactly like it is there > you'll get an error. > > 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: Thursday, April 11, 2019 10:37 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_surf2surf help > > 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://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%7C94991fa8b1e549ea2c9e08d6be93b12c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636905938873837930&sdata=K40k6eVZ40ejC4tNfOrgL%2BWhb6Zh%2FqJwQtpVzpgYM9s%3D&reserved=0 > > On 4/10/19 6:38 PM, Larson, Kathleen E wrote: >> 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%7C94991fa8b1e549ea2c9e08d6be93b12c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636905938873837930&sdata=K40k6eVZ40ejC4tNfOrgL%2BWhb6Zh%2FqJwQtpVzpgYM9s%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%7C94991fa8b1e549ea2c9e08d6be93b12c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636905938873837930&sdata=dY%2BnJIQxhMxco9iSZLCJDE4Fkgc81y4zginC%2BYoSqPM%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%7C94991fa8b1e549ea2c9e08d6be93b12c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636905938873837930&sdata=dY%2BnJIQxhMxco9iSZLCJDE4Fkgc81y4zginC%2BYoSqPM%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%7C94991fa8b1e549ea2c9e08d6be93b12c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636905938873837930&sdata=dY%2BnJIQxhMxco9iSZLCJDE4Fkgc81y4zginC%2BYoSqPM%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%7C94991fa8b1e549ea2c9e08d6be93b12c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636905938873847940&sdata=sAAFUD%2FQLoYSbI4Hv77GhIA%2FyjPFYUdUW51h1H1Pe5Q%3D&reserved=0 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
