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ChristophKirst / ClearMap

ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
http://christophkirst.github.io/ClearMap/build/html/index.html
GNU General Public License v3.0
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Elastix runtime error #44

Open Hesham3esa opened 2 years ago

Hesham3esa commented 2 years ago

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?