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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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RunTimeError - alignData #18

Closed basakakdogan closed 5 years ago

basakakdogan commented 5 years ago

I get the following error when I try to run alignData. Do you have any suggestions?

Thanks.

resultDirectory = alignData(**RegistrationAlignmentParameter); Traceback (most recent call last):

File "", line 1, in resultDirectory = alignData(**RegistrationAlignmentParameter);

File "ClearMap/Alignment/Elastix.py", line 466, in alignData raise RuntimeError('alignData: failed executing: ' + cmd);

RuntimeError: alignData: failed executing: /home/kandellabalien/ClearMap/ClearMap/Elastix/bin/elastix -threads 16 -m /home/kandellabalien/ClearMap/ClearMap/clearmap_ressources_mouse_brain/ClearMap_ressources/25umAutofluoReference/template_25_half.tif -f /home/kandellabalien/ClearMap/Eleanortesthemifromimage450/autofluo_resampled.tif -p /home/kandellabalien/ClearMap/ClearMap/clearmap_ressources_mouse_brain/ClearMap_ressources/Parameter_files/Par0000affine.txt -p /home/kandellabalien/ClearMap/ClearMap/clearmap_ressources_mouse_brain/ClearMap_ressources/Parameter_files/Par0000bspline.txt -out /home/kandellabalien/ClearMap/Eleanortesthemifromimage450/elastix_auto_to_atlas

keithmurphy commented 5 years ago

Did you happen to find a solution to this problem? I saw the other issues thread had issue with using spaces but my directories have only _ and I'm still getting that problem. I'd love any advice you might have.