Hi Donna, I can try to do that. I wonder, still, what kind of input file is expected when using "caret_command -file-convert -fsf2c"? The command's help says it converts "a free surfer functional file" into a metric file, which confuses me a bit. Should it be a volume or something else instead? Best, Pablo
On Wed, Jul 25, 2012 at 11:18 AM, Donna Dierker <[email protected]> wrote: > 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 >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
