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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If > the reader of this message is not the intended recipient or the > employee or agent responsible for delivering the message to the > intended recipient, you are hereby notified that any > dissemination, distribution or copying of this communication is > strictly prohibited. If you have received this communication in > error, please contact the sender immediately and destroy the > material in its entirety, whether electronic or hard copy. Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. 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