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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@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 <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. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline >> <http://www.partners.org/complianceline> . If the e-mail was sent >> to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > =================================== > > > 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). > Visit us online at http://www.clevelandclinic.org for a complete listing of > our services, staff and locations. > > > Confidentiality Note: This message is intended for use only by the > individual or entity to which it is addressed and may contain information > that is privileged, confidential, and exempt from disclosure under applicable > law. 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
