Closed shen4brains closed 3 years ago
@shen4brains I isolated the part of the file manager that handles DWI for quicker and easier debugging. The fileConfig
it generates after processing is as follows:
{'dwi': 'dMRI/raw/dwi.nii.gz', 'dwi_bvec': 'dMRI/raw/dwi.bvec', 'dwi_bval': 'dMRI/raw/dwi.bval'}
looking in my subject's dMRI/raw
directory, it seems like it put those files in the fileConfig
correctly into that directory.
I'm sitll looking at why the files are also being to unclassified but it does seem like the rest of the file manager is processing these correctly, at least for me
The reason it also copies them into /unclassified is that there's a whole code block the first author wrapped in a try-catch statement. If anything at all goes wrong in that statement, it writes all files still in the list the file manager passes in to /unclassified
. *dwi*
specific processing happens before that code block but the code block throws an error because it doesn't find the AP
/PA
directions that the original pipeline is looking for. I added a quick little if-statement at the end that ensures that the *dwi*
files don't also go into /unclassified
because of whatever happens in the try-catch block. Issue fixed with https://github.com/McIntosh-Lab-RRI/tvb-ukbb/commit/b1234c28e030c90d90c13aa0c373dc94843228a7
file manager detects *dwi.nii.gz filenames fine but then places dwi files in /unclassified directory and no processing of dwi is performed
for an example, see here: /liberatrix/mcintosh_lab/kshen/ukbb_test/camCAN/sub-CC222797
here is the code block it should not enter: https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/8a23e5a741a9188067be8ca3ebfea4736d25a2e0/bb_pipeline_tools/bb_file_manager.py#L546