Utility to combine rois in neuroimaging atlases
This initial version of the tool supports 3D non-probabilistic atlases with sequential Region of Interest (ROI) numbers used to represent brain areas starting from 1. When two or more ROIs are merged into one then the smallest original ROI number is used to respresent the new merged ROI.
customize-atlas.py can be run from the command line as follows:
python3 customize-atlas.py [atlas_filename] [label_filename] [assignment_filename] --new_atlas_file [my_new_atlas_filename] --new_label_file [my_new_label_filename]
where
[atlas_filename] is the file path of the original atlas file
[label_filename] is a text file that contains each roi label on a single text line (see Brainnetome_basic.txt in brainnetome-example folder)
[assignment_filename] is a text file that assigns a new roi to a set of existing roi labels on a single text line without spaces (see assign.txt in brainnetome-example folder)
So for example the line:
HippAmyg_LR_21_21=Hipp_L_2_2,Hipp_R_2_2,Amyg_L_2_1,Amyg_R_2_1
will create a new ROI called HippAmyg_LR_21_21 from the ROIs Hipp_L_2_2, Hipp_R_2_2, Amyg_L_2_1 and Amyg_R_2_1.
In this example because Amyg_L_2_1 has the smallest ROI number (i.e. 211 as determined from the label file Brainnetome_basic.txt) then the new ROI will initially have 211 as its ROI number. Of course this could change if additional assignments in the assignment file cause knock-on changes.
if --new_atlas_file and --new_label_file are not defined then the changed atlas file is automatically stored using the original filename with _custom.nii.gz as the suffix. The same will occur with the label file with _custom.txt as the suffix.
Testing can be carried out on the provided example as follows:
python3 customize-atlas.py BNA-maxprob-thr0-2mm.nii.gz Brainnetome_basic.txt assign.txt my_new_atlas.nii.gz my_new_label.txt`
python3 -m pdb customize-atlas.py BNA-maxprob-thr0-2mm.nii.gz Brainnetome_basic.txt assign.txt