It might be simpler to map a functional NIFTI volume onto your subject's surface resampled to the F99 mesh. The functional volume must be in register, volumetrically, with the anatomical used to segment the surface. And there might be issues with orientation (e.g., volume is coronal, while surface is left-to-right, posterior-to-anterior, inferior-to-superior). But at least hypothetically you could rotate/flip your surface to the same orientation as your volume (saving the coord by a different name).
In your steps 1 and 2 below, something seems funky, because the output should be something like a freesurfer .w file -- not a surface. Surfaces don't equate to metrics -- .w files do. I don't know how to create .w files in freesurfer. On Jul 24, 2012, at 8:08 PM, Pablo Polosecki wrote: > Dear List, > > I managed to register my FreeSurfer macaque surface to Caret's F99 > atlas, following and modifying the scripts in the FS-to-F99 tutorial. > I would like now to overlay on it my functional activations generated > by FreeSurfer, which I have as a volume in nifti format. My approach > is the following: > > 1-Convert my functional map from volume into surface. I accomplish > this using FreeSurfer's mri_vol2surf command. > 2-Convert the resulting FreeSurfer surface into a Caret surface. For > this I plan on using: > caret_command -file-convert -fsf2c $input_FS_functional_surface > $input_FS_inflated_surface $output_caret_metric_surface -stuch > $hemisphere > 3-Take the resulting caret metric surface and apply to it the > transformation matrix to convert to F99 coordinates (this > transformation matrix has been previously calculated by scripts in the > FS-to-F99 tutorial) > 4-Add resulting surface to > my_macaque.$hemisphere.Registered-to-F99.74k_f99.spec > > Please correct me if you know a simpler approach, I'm new to Caret. In > any case, my problem is with step 2. I get the following error: > FILE CONVERSION ERROR: Error > /Volumes/Polac/Desktop/fs-to-f99/120509GIZMO/func_surface/sig-rh.mgh: > Functional data found for node with index larger than there are nodes > in the surface. > > I don't know why this happens: FreeSurfer can overlay this surface > file with no complains on my FS inflated surface. Do you know a > possible workaround? > > Thank you very much! > Pablo Polosecki > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
