ROI_legends = "/mnt/paros_MRI/jacques/atlases/IITmean_RPI/IITmean_RPI_index.xlsx"
elif 'santorini' in computer_name:
# mainpath = '/Users/alex/jacques/'
mainpath = '/Volumes/Data/Badea/Lab/human/'
ROI_legends = "/Volumes/Data/Badea/ADdecode.01/Analysis/atlases/IITmean_RPI/IITmean_RPI_index.xlsx"
elif 'blade' in computer_name:
mainpath = '/mnt/munin6/Badea/Lab/human/'
ROI_legends = "/mnt/munin6/Badea/Lab/atlases/IITmean_RPI/IITmean_RPI_index.xlsx"
else:
raise Exception('No other computer name yet')
# target_tuple = (24,1)
# target_tuple = [(58, 57)]
# target_tuples = [(64, 57)]
ratio_str = ratio_to_str(ratio)
print(ratio_str)
if ratio_str == '_all':
folder_ratio_str = ''
else:
folder_ratio_str = ratio_str.replace('_ratio', '')
# target_tuple = (9,77)
_, _, index_to_struct, _ = atlas_converter(ROI_legends)
if project == 'AMD':
mainpath = os.path.join(mainpath, project)
groups = [
'Initial AMD', 'Paired 2-YR AMD', 'Initial Control',
'Paired 2-YR Control', 'Paired Initial Control', 'Paired Initial AMD'
]
trk_fixer(trk_path, trk_newpath, verbose=True)
else:
print(f'Already fixed {trk_name}')
trk_folder = TRK_output
new_trk_folder = '/mnt/paros_MRI/jacques/AD_Decode/Analysis/TRK_MPCA_neworient_fixed_100/'
mkcdir(new_trk_folder)
ratio = 100
filelist = os.listdir(trk_folder)
#filelist = sorted(filelist)
filelist.reverse()
for filepath in filelist:
filename, f_ext = os.path.splitext(filepath)
ratio1 =get_ratio(filepath)
ratio2 = int(ratio1*ratio)
filename2 = filename.replace(ratio_to_str(ratio1),ratio_to_str(ratio2))
newfilepath = os.path.join(new_trk_folder, filename2 + f_ext)
if not os.path.exists(newfilepath):
print(f'Downsampling from {os.path.join(trk_folder,filepath)} to {newfilepath} with ratio {str(ratio)}')
#print(f'{filename} converted to {filename2 + f_ext}')
reducetractnumber(os.path.join(trk_folder,filepath), newfilepath, getdata=False, ratio=100, return_affine= False, verbose=False)
print(f'succesfully created {newfilepath}')
else:
print(f'already created {newfilepath}')
"""
if testing:
trk_test = '/Users/alex/jacques/AMD_TRK_testing/TRK/H21850_stepsize_2_ratio_100_wholebrain_pruned.trk'
trk_new = '/Users/alex/jacques/AMD_TRK_testing/TRK/H21850_ratio100_fixed.trk'
trk_fixer(trk_test, trk_new, verbose=True)
else: