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#directory of the alig'/home/nicolas.renier/Documents/ClearMap_Ressources/Par0000affine.txt',nment result
"result_directory" : ws.filename('resampled_to_auto')
};
elx.align(**align_channels_parameter);
and i am getting this error:
runcell('Aignment - resampled to autofluorescence', '/home/hesham/ClearMap2/ClearMap/Scripts/CellMap.py')
Traceback (most recent call last):
File "/home/hesham/ClearMap2/ClearMap/Scripts/CellMap.py", line 143, in
elx.align(**align_channels_parameter);
File "/home/hesham/ClearMap2/ClearMap/Alignment/Elastix.py", line 552, in align
raise RuntimeError('align: failed executing: ' + cmd);
Hello I am trying to run this code
#%% Aignment - resampled to autofluorescence
align the two channels
align_channels_parameter = {
#moving and reference images
"moving_image" : ws.filename('resampled', postfix='autofluorescence'),
"fixed_image" : ws.filename('resampled'),
#elastix parameter files for alignment
"affine_parameter_file" : align_channels_affine_file,
"bspline_parameter_file" : None,
#directory of the alig'/home/nicolas.renier/Documents/ClearMap_Ressources/Par0000affine.txt',nment result
"result_directory" : ws.filename('resampled_to_auto')
};
elx.align(**align_channels_parameter);
and i am getting this error:
runcell('Aignment - resampled to autofluorescence', '/home/hesham/ClearMap2/ClearMap/Scripts/CellMap.py')
Traceback (most recent call last):
File "/home/hesham/ClearMap2/ClearMap/Scripts/CellMap.py", line 143, in
elx.align(**align_channels_parameter);
File "/home/hesham/ClearMap2/ClearMap/Alignment/Elastix.py", line 552, in align
raise RuntimeError('align: failed executing: ' + cmd);
RuntimeError: align: failed executing: /home/hesham/ClearMap2/ClearMap/External/elastix/build/bin/elastix -threads 16 -m /media/hesham/Extra/1.1 final/resampled_autofluorescence.tif -f /media/hesham/Extra/1.1 final/resampled.tif -p /home/hesham/ClearMap2/ClearMap/Resources/Alignment/align_affine.txt -out /media/hesham/Extra/1.1 final/elastix_resampled_to_auto
does anyone have an idea how to fix?
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