Thank you! So good news, that worked and created wmparcSlh.w I'm not sure what the .w means. When I try to load it onto the surface, I get an error: "Failed to load Surface overlay."
Thank you, Anna ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca] Sent: Friday, September 30, 2016 12:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface My apologies, I meant "--regheader subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface hmmm, yup not sure there. Did you try "--regmethod subject" -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: Just to make sure I am actually doing what you are suggesting my input and output is below. Thanks, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --reg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg --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/surf/lh.sphere.reg 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 inplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.sphere.reg ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 12:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Did you try --regmethod subjid? or --reg sphere.reg ? If that doesn't work then I'm not sure how to help - Bruce or Doug, any thoughts? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: I am still having problems. If I do --reg subject I get an error back that it is a directory. If I pick a specific file such as orig.mgz (default according to help file), I get the same error as before. Thanks, Anna ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 11:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface Gotcha, so when I was trying to do something similar I used mri_vol2surf with --regmethod subjid since you don't actually want to perform a transformation. Maybe try that? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna <crawf...@ccf.org<mailto:crawf...@ccf.org>> 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@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 <crawf...@ccf.org<mailto:crawf...@ccf.org>> wrote: I already ran recall-all. I am trying to create a different surface not created using recon-all. Anna ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>] Sent: Friday, September 30, 2016 10:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Volume to Surface You 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 <crawf...@ccf.org<mailto:crawf...@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 =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). 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