Dear Brinstormers,
I have a thalamic maps obtained from diffusion which look-up table with colours and labels in FSLeyes format. Is there a way to have the same table imported in Brainstorm? If not, what is a LUT file format for Brainstorm so I can manually crate one for all subjects.
Thank you for your help.
Best,
Jacek
You would like to import this where, how and to do what?
Can you please be more explicit on what you'd like to do?
Including some figures may help explaining your objectives.
Thanks
Dear Francois,
Sorry for being too vague! Let me break down what I want to do.
We created a nii.gz mask with 12 areas in FSL, which has a complimentary lookup table with the names and colours for these areas, which we would like to use in Brainstorm analysis too. I created a new volume scouts atlas, and imported the nii.gz mask, using "Volume mask or atlas (dilated, subject space)" option and get all the areas into BS. However, they get randomly assigned colours and only numerical values.
Is there a way to make a look-up table that will be used during the import or point BS towards it after? And if so, what is the format of the LUT?
Thank you for your help,
Jacek
Thank you for the explanation.
No, unfortunately, it is not possible to add information from an external LUT file when reading a custom volume as an atlas.
The easiest might be for you to write a Matlab script to replace the color and label for each scout in the atlas "C17_ftb_n_sp.nii" after loading it, directly in the structure of the cortex file.
The scouts/atlas structure is described here:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scouts#On_the_hard_drive
The introduction tutorial "Scripting" describes various ways for editing Brainstorm data structures manually (use in_tess_bst for reading a surface file):
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Example:_Editing_events
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Reference:_File_manipulation
You can find code to read the .lut files in this function:
