| #!/usr/bin/python | |
| # Create bitmaps to check defacing of all NIFTI images | |
| # python bids_deface_bitmaps.py | |
| from pathlib import Path | |
| import os | |
| import os.path | |
| import glob | |
| import sys | |
| import shutil | |
| import fnmatch | |
| def remove_after_final_underscore(input_string): | |
| # Find the last underscore index | |
| last_underscore_index = input_string.rfind('_') | |
| # If an underscore is found, remove characters after it | |
| if last_underscore_index != -1: | |
| result_string = input_string[:last_underscore_index] | |
| return result_string | |
| else: | |
| # If no underscore is found, return the original string | |
| return input_string | |
| if __name__ == "__main__": | |
| inputRoot = './' | |
| outRoot = './bmps/' | |
| exe = '/Applications/MRIcroGL.app/Contents/MacOS/MRIcroGL' | |
| if not shutil.which(exe): | |
| sys.exit("Unable to find exe: "+exe) | |
| nifti_files = [f for f in os.listdir(inputRoot) if fnmatch.fnmatch(f, 'wsub-M4209*.nii.gz')] | |
| for subname in list(nifti_files): | |
| sub = Path(subname).stem | |
| les = os.path.join(inputRoot, subname) | |
| #wbsub-M2185_ses-388_T1w.nii.gz | |
| T1 = remove_after_final_underscore(sub) | |
| bmp = os.path.join(outRoot, T1 + ".png") | |
| T1 = T1[:1] + 'b' + T1[1:] + '_T1w.nii.gz' | |
| T1 = os.path.join(inputRoot, T1); | |
| if not os.path.isfile(T1): | |
| print('oops: '+ T1); | |
| continue | |
| #print(T1) gl.overlayload | |
| cmd = exe + ' -s \'import gl\ngl.loadimage("' + T1 + '")\ngl.drawload("' + les + '")\ngl.mosaic("A 0.5 S 0.25 C 0.5 S R -0")\ngl.colorbarposition(0)\ngl.savebmp("' + bmp + '")\ngl.quit()\'\n' | |
| os.system(cmd) | |
| #sys.exit() | |