Thank you, Bruce.
I did reconstruct the surfaces from that subject. These are the steps that I've taken: recon-all -s <subid> -i <mprage> -all mris_register <subid>/surf/<hemi>.sphere fsaverag5/<hemi>.?reg.template.tif <subid>/surf/<hemi>.fsaverage5.sphere.reg mri_surf2surf -s <subid> -h <hemi> --sval-xyz <hemi>.pial --trgsubject fsaverage5 --tval <hemi> mri_surf2surf -s <subid --hemi <hemi> --sval-xyz <hemi>.pial --trgsubject fsaverage5 --tval <hemi>.pial.<subid> --tval-xyz <subid>/mri/orig.mgz mris_convert fsaverage5/surf/<hemi>.pial.<subid> fsaverage5/surf/<hemi>.pial.<subid>.asc this final file (fsaverage5/surf/<hemi>.pial.<subid>.asc) was read into MATLAB and MATLAB code generates a continuous value for each vertex (n=10242) for a given subject. I want to map these values back to the surface, but it sounds like if you're recommending mri_vol2surf, that you are saying I should represent these continuous values in a voxel in 3D space, is that correct? Is there an easy way to map the values for each vertex without having to go through a 3D representation? Best, Fred Hi Fred we usually use mri_vol2surf for this kind of thing. Did you reconstruct surfaces from that subject? cheers Bruce On Tue, 13 Feb 2018, Frederick Barrett wrote: Greetings all, I apologize in advance for what may (or may not) be a basic question. I want to map values from a continuous variable (non-integer) to each vertex on a surface so that I can visualize these values on the surface (or an inflated brain), but I can't figure out how to do this. I've projected the pial surface of fsaverage5 to native space within a volunteer, then exported the xyz coordinates of each vertex (10242 * 2, lh & rh) for that volunteer to an .asc file using mris_convert. These xyz coordinates (and the vertex #) and a 3D summary volume (NIfTI) for a BOLD scan in native space for the subject were read into MATLAB, and I've used a separate toolbox in Matlab to generate weights from the BOLD data that map to each vertex (a continuous variable, one weight per vertex per subject), and these weights can be written to a text file in the following format for each hemisphere: x1 y1 z1 weight1 x2 y2 z2 weight2 ... x10242 y10242 z10242 weight10242 or vertex1 weight1 vertex2 weight2 ... vertex10242 weight10242 or another format if that would be helpful. How can I map these weights back to a surface and visualize it? Please advise. I began to think this fell into the realm of annotation, but it seems that annotations are categorial rather than continuous. Thank you so much for your time. Best, Fred ---------------------------------------------------------- Frederick Barrett, Ph.D Assistant Professor of Psychiatry and Behavioral Sciences Behavioral Pharmacology Research Unit Johns Hopkins School of Medicine 5510 Nathan Shock Dr / Rm 3048 Baltimore, MD 21224 Voice/mail: (410) 550-9777 Email: fbarr...@jhmi.edu | frederick.barr...@gmail.com NCBI: https://goo.gl/mUKEZm Google Scholar: MailScanner has detected a possible fraud attempt from "scholar.google.com" claiming to be http://goo.gl/vjrrsl _______________________________________________ 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.
_______________________________________________ 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.
