No CommandLine option "-out" given!

[vzickus]

Get this error (in the title) before RuntimeError('alignData: failed executing: ' + cmd) is raised (however, I cannot track the reason down). Any ideas? For some reason, the

res = os.system(cmd)

returns res = os.system(cmd)

Traceback:
File "process_template.py", line 26, in
resultDirectory = alignData(**RegistrationAlignmentParameter)

I wonder if this could have anything to do with the "bleed" in atlas. However, I believe I just used the default settings provided in the tutorial, and by eye the atlas and the LSFM data look of similar size.

[jmmanley]

Hi,
Christoph should know better, but this error could be caused if you are not giving the proper output path in your alignment parameters. What are you using for RegistrationAlignmentParameter["resultDirectory"]?

This error could be due to no path given after the -out flag when it tries to run the Elastix command (lines 455-461 in Alignment/Elastix.py):
cmd = ElastixBinary + ' -threads 16 -m ' + movingImage + ' -f ' + fixedImage + ' -p ' + affineParameterFile + ' -out ' + resultDirectory

[vzickus]

I can see that the resultsDirectory is successfully created, but empty. I'll have to search for other hard-coded paths that I might have missed in the tutorial. I'll keep you updated.

[vzickus]

I could not find any hard-coded bits, and when I print out "RegistrationAlignmentParameter", the paths seem correct. I wonder if it has something with the fact that the bottom of the images look crazy ( https://www.dropbox.com/s/6shi2gubb3uujds/autofluo_for_cfos_resampled-single.tif?dl=0 ) and I have not cropped them...

[vzickus]

I tested elastix separately (that is, just elastix on its own from terminal) on the same images, and it worked without issues. Updated: I think the cause was simply a space " " in the directory structure (probably required a r"path\to\folder with\space"). Closing, and thanks for your help.

[auesro]

For future users:
The folders' names, inside the downloaded ClearMap Resources folder, are separated by spaces while the code looks for names in which the spaces have been replaced by underscores "_".