Hi all.
(apologies to those on both free surfer & caret list serves)
I've having issues trying to convert some regions that are in .label.gii format. I'm trying to take them from Caret 164k mesh space into fsaverage space to be viewed on Free Surfer. I've successfully brought similar data the opposite direction, but for some reason I'm unable to go in the reverse. I've outlined my initial steps very briefly and go into further detail when I get to the areas where it appears that the (a) problem is.
Steps: Load the spec file. The 'label.gii' can be loaded with the spec file, but it doesn’t really matter. I save this file as a .paint file first, so that it can be deformed, as in the Apply Deformation Map options there is no option for .label.gii only .paint.
This could be a potential issue as the the packages I'm using are all originally in .gii format. I'm new to working with files in the .gii format. Does this file format present any issues with commands such as caret_command. I know I've had to do workarounds as the 'Apply Deformation Map' box does not appear to support .label.gii, .coord.gii, etc files. Am I wrong with this or is there a better way to deal with this issue?
Apply the deformation map: 'fsaverage.L.registered-to-fs_LR.164k_fs_LR.deform_map'
Here is where I think the problem is: The caret_command should be able to convert this into a series of .label files. The caret_command help box offers this: -file-convert -cp2fsl Convert a paint file into free surfer label files. No output name is needed since free surfer uses on file per paint ID with the name of the file being "paintID" label. Here is the command line I've been using: caret_command -file-convert -cp2fsl fs_L-to-fs_LR_Power_et_al_Neuron11.L.164k_fs_LR.paint Help-me-please.coord
So, this command has been extracting the .label files. But when viewed in tksurfer, they are distorted. It seems to me that the issue is the .coord file. I've tried the .coord file that was with the spec file, but it was in original 164k mesh space. So I also tried to apply the same deformation map to the .coord after. In order to do this I saved the .coord.gii file as .coord file first, then applied the map . Still to no avail. I'm not sure what is the best .coord file to use, as I've tried multiple combinations of different .coord files and deform maps.
Any help would be much appreciated. Thanks in advance.
-Sam