Hi Donna, I finally did it. In case it helps anyone in the future, it turns out you can save your "surface-ized" version in ".w" format for your functional volume activation using mri_vol2surf. You must give it "paint" as the output format option.
Thanks again, Pablo On Wed, Jul 25, 2012 at 2:03 PM, Pablo Polosecki <[email protected]> wrote: > 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
