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
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