Hesham3esa
commented
2 years ago now it is saying this ERROR: could not read fixed image. both -f and -f0 are unspecified Errors occurred!
Open Hesham3esa opened 2 years ago
Hesham3esa
commented
2 years ago now it is saying this ERROR: could not read fixed image. both -f and -f0 are unspecified Errors occurred!
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?