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1_mask_priori_ROI.py
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1_mask_priori_ROI.py
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#!/bin/python
#################################################
## 1. create ROI mask from coordinates
## Definition Area
#################################################
output_dir = '/home/clancy/data/LesionBrainMapping/ROIs'
csv_file = '/home/clancy/data/LesionBrainMapping/sample_data/sample_coordinates.csv'
roi_radius = 6
#################################################
## Run
#################################################
import os
from brainmapping.functions import make_sphere_from_coords_in_csv
if not os.path.exists(output_dir):
os.mkdir(output_dir)
make_sphere_from_coords_in_csv(csv_file, roi_radius, output_dir)
#################################################
## 2. create ROI mask from maps
## Definition Area
#################################################
maps_dir = '/home/clancy/data/LesionBrainMapping/ROIs'
threshold = 0.5
output_dir = '/home/clancy/data/LesionBrainMapping/ROIs'
#################################################
## Run
#################################################
import os
from brainmapping.functions import make_sphere_from_maps
if not os.path.exists(output_dir):
os.mkdir(output_dir)
make_sphere_from_maps(maps_dir, threshold, output_dir)
## end. author@kangwu