yes, that's right. You will use mri_vol2surf with the identity matrix with the parcellation, but some bbregister-generated .dat file with PET data.
cheers Bruce
On Fri, 30 Sep 2016, Crawford, Anna wrote:
No problem. I'm not exactly sure, but I think I just want a surface overlay so mri_vol2surf would be what I want. Right now, I am just trying to get down the generic way of how to do it which is why I went with trying to overlay the parcellation onto the inflated surface. Later, I will have different modalities such as PET that I will want to overlay on the inflated surface that will already be registered to the MRI. So I just wanted to get the proper workflow of how to get a volume overlayed onto the surface if that makes sense.
Thank you, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:48 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface
Sorry - always helps to read the whole question :D
So, you are trying to create an inflated white surface? As far as I know this doesn't exist. Freesurfer creates white surfaces, pial surfaces, and inflated surfaces that are the pial pushed outwards.
Also, "mri_vol2surf" creates surface overlays on surfaces that already exist.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all.
Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to SurfaceYou have to run recon-all to get the surfaces of a volume.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Sep 30, 2016 at 9:47 AM, Crawford, Anna CRAWFOA4@ccf.org wrote: Hello,
I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat===================================
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