or better yet, use our naming conventions an dcall it lh.wmparcS.mgh (or .mgz)
On Fri, 30 Sep 2016, Douglas N Greve wrote: > Anna, try removing --out_type paint and instead specify the output file > as wmparcSlh.mgh > > Trisanna, thanks so much for chipping in! > > > > On 09/30/2016 01:14 PM, Trisanna Sprung-Much wrote: >> Ok so this is where my knowledge might be limited because you did a >> slightly different thing than me by specifying the output type as >> "paint" - that is what the .w format is. This is a label, I believe >> and needs to be loaded as such. >> >> What happens if you try to remove the "output_type" and try to load >> the result as an overlay? >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Fri, Sep 30, 2016 at 1:00 PM, Crawford, Anna <crawf...@ccf.org >> <mailto:crawf...@ccf.org>> wrote: >> >> 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 >> <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 12:51 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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