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 [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<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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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<mailto: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<mailto: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 . 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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 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). 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