I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a similar type of surface to the one I had sent.
mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh --regheader segfs --hemi lh --surf white --out_type mgh --projfrac 0.5 srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+aseg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/mri/orig.mgz as target reference. Reading surface /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.white Done reading source surface Reading thickness /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt//segfs/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 73174 Writing to /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/lh.aparc+asegS.mgh Dim: 115984 1 1
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
You should use aparc+aseg.mgz and set the --projfrac 0.5. This should produce something with the same information as the ?h.aparc.annot (though the color scale will be different)
On 09/30/2016 03:51 PM, Crawford, Anna wrote:
I was just using the wmparc as an example to get a volume overlay onto the surface. I chose that one just to see the parcellated surface similar to the volume. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 3:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
I can't tell from that image if it is right. Why are you mapping the wmparc to the surface? The wmparc will have segmentation boundaries right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
Thank you everyone for your help! I do have a follow up question. I believe this did what I wanted and is what I will want to do for PET data for example. When I did the wmparc to the surface, I was expecting to see the different areas mapped out similar to the volume. I have attached a screen capture of what it looks like. Can someone confirm that this seems to be correct and I was just expecting the wrong thing? I suspect this is the case since to see the different areas in the volume you use the look up table for the color map and that is not an option for the surface overlay.
Thank you all again for your feedback!
Anna ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, September 30, 2016 2:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Volume to Surface
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 <CRAWFOA4@ccf.org mailto:CRAWFOA4@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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@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 <CRAWFOA4@ccf.org <mailto:CRAWFOA4@ccf.org>> wrote: Yeah, I get Error: Option unknown for --regmethod Anna ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@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 <CRAWFOA4@ccf.org <mailto:CRAWFOA4@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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@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 <CRAWFOA4@ccf.org <mailto:CRAWFOA4@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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@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 <CRAWFOA4@ccf.org <mailto:CRAWFOA4@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-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto: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 <mailto: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 <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Trisanna Sprung-Much [trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@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 <CRAWFOA4@ccf.org <mailto: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 =================================== 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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