Hi All, I'm trying to project some processed resting-state data onto the surface to run some surface based parcellations, and I'm running into a bit of difficulty. Basically I'm using bbregister to register my functional to the T1, then mri_vol2surf to project to the surface with the following pseudocode:
bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \ --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \ --init-fsl --bold mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \ --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \ --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \ --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh --noreshape The registration looks pretty good after I run bbregister, but what I get out from the mri_vol2surf seems weird. First of all, the dimensions are 112745 x 1 x 1 x 120, which seems odd. I'm forcing no reshaping, and from the help page it seems like the x-dim should be 40962 for icoorder=6. I have 120 frames in my input data, so that seems to be right, but I'm not sure where this dimension is coming from. I've also tried it with icoorder=4 and I get the same x-dim=112745 when I'm expecting 2562. I've also run these commands with various iterations e.g. reshaping, no smoothing, no projfrac, and I get the same thing every time. I'm also wondering how I should view these files to confirm that the surface projection has worked as I expect it if/when I am able to get the dimensions to be correct. I cannot open any of the projected functional files in either freeview or tksurfer, so it will be helpful to know how I might be able to view these time-series on the surface after I've succeeded in projecting them to that space. Any advice would be much appreciated Thanks, Jared _______________________________________________ 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.
