Sam, It is possible to carry out the conversion you desire in a single step. First, some clarifying comments.
1) What you call 'Caret 164k mesh' is what we call the '164k_fs_LR' mesh, to signify that it is derived from registering the fsaverage left hem (164k_fs_L mesh) and right hem (164k_fs_R mesh) to a common 'fs_LR' hybrid target. 2) You were using a deformation map (fsaverage.L.registered-to-fs_LR.164k_fs_LR.deform_map) that registers in the opposite direction from what you want (i.e., it registers data FROM the fs_L mesh TO the fs_LR mesh). What you want is the deformation map that goes FROM fs_LR TO fs_L. 3) A complete set of deformation maps and associated files needed to register from fs_L to fs_LR and vice versa, from fs_R to fs_LR and vice versa, and also between fs_LR and pals_L/pals_R are available in SumsDB: http://sumsdb.wustl.edu/sums/directory.do?id=8291757&dir_name=Inter-atlas_deformation_maps 4) The README.inter-atlas-registration_March2012.txt in this directory gives some tips on how to proceed. The archive inter-atlas_deformation_maps.zip contains the files you need and unzips to the appropriate directory structure. 5) caret_command -deformation-map-apply can in fact convert label.gii files (even though this is not advertised, and even though the Caret5 Apply Deformation Map does not work for this purpose). For example, I successfully converted the file you are interested in (Power_et_al_Neuron11.L.164k_fs_L.label.gii) with the following command caret_command -deformation-map-apply fsaverage.LR.registered-to-fs_L_fix.164k_fs_L.deform_map PAINT /Users/vanessen/BRAIN_MAP_DATA/human_atlas-fs_LR/atlas_Conte69_164k_fs_LR/Power_et_al_Neuron11.L.164k_fs_LR.label.gii Power_et_al_Neuron11.L.164k_fs_L.label.gii I hope this now works for you - and others. David VE On May 4, 2012, at 6:10 PM, Sam Carpenter wrote: > 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 > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users
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