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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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Content hashing for renamed working directory #37

Closed binarybottle closed 10 years ago

binarybottle commented 10 years ago

When I rename the working directory from "/Users/arno/Desktop/working" to "/Users/arno/Desktop/working2" and try to rerun the command:

mindboggle OASIS-TRT-20-1 --ants_data ~/Data/antsCorticalThickness tmp -n 6 --freesurfer_data /desk/subjects --working /desk/working2 --out /desk/output2 --no_surfaces --thickness

I get an error:

"No such file or directory: '/Users/arno/Desktop/working/Mindboggle/_subject_OASIS-TRT-20-1/labels_mgh_to_nifti/wmparc.nii.gz"

related to the following line in the mindboggle file:

https://github.com/binarybottle/mindboggle/blob/master/mindboggle/mindboggle#L1771

Why is it looking in the old directory for this file?

satra commented 10 years ago

to be able to move directories you need to configure use_relative_paths to be true, or update the hashes with wf.run(updatehash=True). why do you want to change the working directory again? this wasn't intended to be common behavior in nipype.

binarybottle commented 10 years ago

The Stony Brook lab needs to move the working folder around as part of its data management system.

After trying both settings, I still get the same errors -- it's still looking in "working" as opposed to "working2"...

binarybottle commented 10 years ago

Submitted an issue on nipype's github site: https://github.com/nipy/nipype/issues/734