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> 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 [ > 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> wrote: > >> Yeah, I get Error: Option unknown for --regmethod >> >> 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 12:41 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> >> 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/Brai >>> nStem/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/m >>> ri/wmparc.mgz >>> srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/s >>> urf/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/Brai >>> nStem/study11074/S2sdt/segfs/surf/lh.sphere.reg >>> ------------------------------ >>> *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 12:08 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> >>> 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 [ >>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna >>>> Sprung-Much [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> >>>> 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 [ >>>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna >>>>> Sprung-Much [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> >>>>> 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 [ >>>>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Trisanna >>>>>> Sprung-Much [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> >>>>>> 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/Brai >>>>>>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out >>>>>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh >>>>>>> --srcreg /mnt/netScratch/crawforda/Brai >>>>>>> nStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white >>>>>>> --out_type paint >>>>>>> INFO: output format is paint >>>>>>> srcvol = /mnt/netScratch/crawforda/Brai >>>>>>> nStem/study11074/S2sdt/segfs/mri/wmparc.mgz >>>>>>> srcreg = /mnt/netScratch/crawforda/Brai >>>>>>> nStem/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/Brai >>>>>>> nStem/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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Thank you. >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> 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 . 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. >>>> >>>> >>> =================================== >>> >>> 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 >>> >>> >>> 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 . 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. >>> >>> >> =================================== >> >> 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 >> >> >> 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 . 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. >> >> > =================================== > > 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 > > > The information in this e-mail is intended only for the person to whom it > is > addressed. 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