DOC: Example that explores BIDS and includes tractography from another pipeline.

[arokem]

@jyeatman : this is the example that shows how to use tractography outputs from another pipeline

[arokem]

I think there's something wonky with this trk file. I get:

In [5]: img = nib.load("/Users/arokem/AFQ_data/stanford_hardi/derivatives/vistas
   ...: oft/sub-01/ses-01/dwi/sub-01_ses-01_dwi.nii.gz")

In [6]: load_tractogram("/Users/arokem/AFQ_data/stanford_hardi/derivatives/my_tr
   ...: actography/sub-01/ses-01/dwi/sub-01_ses-01-dwi_tractography.trk", img)
WARNING:root:Dimensions must be above 0.
WARNING:root:Dimensions must be above 0.
WARNING:root:Dimensions must be above 0.
ERROR:root:Affine not equal
ERROR:root:Dimensions not equal
ERROR:root:Voxel_size not equal
ERROR:root:Trk file header does not match the provided reference.
Out[6]: False

[arokem]

Thanks for the comments. I think they're addressed in the last couple of commits, but let me know if you think I should be more specific about anything.

[arokem]

On a bit of further thought, I think that this example could be expanded a bit to explain how/why we use BIDS more generally. Hopefully, I'll find some time to work on that tomorrow. And also to fix the failing test.

[bloomdt-uw]

May want to identify any files that are under bids that cannot be located, do not conform to standards, and do not follow convention. If pybids doesn't support this we may want to open an issue.

In lieu can:

• run bids-validator
• run bids_layout.get() and compare to an os.walk
• run get_entities()

[bloomdt-uw]

May want to include primer on how to configure/diagnose bids_filters:

bids_layout = BIDSLayout(BIDS_DIR, derivatives=True)
# find all files
bids_layout.files
# get a specific file; probably want to specify full path
bids_layout.get()
# find out what entities are available for bids filters for file
bids_layout.get().get_entities()

Some issues have been dataset_description.json, file naming convention doesn't uniquely identify file with bids filters, ...

[pep8speaks]

Hello @arokem! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file AFQ/data.py:

Line 1642:80: E501 line too long (80 > 79 characters)

Comment last updated at 2020-11-19 06:22:47 UTC

[arokem]

Reading this and the comments again, I think that maybe this is enough for now? I think that a more detailed tutorial on BIDS/pyBIDS is out of scope for us, and users can get more information from the pybids documentation. So, I think this is ready for another review and potentially even merge.

[36000]

LGTM!