Hi, I want to use rawfunc2surf-sess to project the functional data onto the surface in the source subject and then in the target subject. My source subject has been processed in Freesurfer. However, my target subject has been processed in Caret, so I do not have all the surface files for the target subject. To get rawfunc2surf-sess to work for my situation, I have to make some minor changes in its code. By looking at the code, I realized that rawfunc2surf-sess calls mri_vol2surf for mask and raw data, then it calls mris_fwhm to smooth raw data within mask. I am describing the changes that I have to make in these two commands, plus a specific question for each change:
1) mri_vol2surf includes the --cortex flag. Since I do not have cortex.label in the target subject, I am removing this flag. Would this be problematic later on? I will eventually do specific analyses on the occipito-temporal vertices in Matlab. Since I have lobar labels in the target subject, I can select/mask those vertices later on. 2) For the source subject, I have the white and pial surfaces. For the target subject, I have the midthickness surface which is somewhere between white and pial. I am adding --surf midthickness in mri_vol2surf to specify the target surface to be midthickness (instead of white). Will this be a problem when the source subject does not have such surface? 3) There is --projfrac 0.5 in mri_vol2surf. The help says "When [the projfrac is] set at 0.5 with the white surface, this should sample in the middle of the cortical surface. This requires that a ?h.thickness file exist for the source subject". I have the thickness file in the source subject - though I don't have it in the target subject. Does 'projfracing' happen only for the source subject? 4) I assume that mris_fwhm will work fine for my situation, unless it requires the white surface in the target subject. Which file is used in mris_fwhm for extracting the vertices coordinates? Thanks in advance for your advice, Reza _______________________________________________ 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.
