Add fwDTI #931
Add fwDTI #931
Conversation
AFQ/tasks/data.py
Outdated
| @as_img | ||
| def fwdti(brain_mask, data, gtab): | ||
| """ | ||
| full path to a nifti file containing parameters |
There was a problem hiding this comment.
This docstring needs to be edited.
There was a problem hiding this comment.
We just need a description, not the parameter section for this function
|
Remaining work:
|
arokem
changed the title
|
I think this is mostly done. Any ideas on where to add this to existing testing? I am thinking of adding it to the list of already calculated scalars in |
|
New test errors might be related to the new release of numpy that happened yesterday. |
|
It looks like all that remains here is the OR example: https://github.com/yeatmanlab/pyAFQ/actions/runs/3741923319/jobs/6352177395#step:5:1817, which also seems broken on master. It's puzzling, because it works locally for me. We might be into similar issues to what we are seeing with the SLR tests, where we don't actually have control over the randomness generated by probabilistic tracking. I think I'm going to try deterministic tracking here and see whether that works. |
This is because combine_bundle requires a syn registration.
Also, adds a space in the error message in GroupAFQ.
|
Looks like using the HBN data sorted out the OR example issues! I wonder if it would sort out our SLR woes as well... I still need to figure out how to embed the montage image in the example webpage. I might do that tomorrow. |
|
When this is done, let me know so I can rebase #937 on top of this, and see if it works then. I think SLR works there now, I just need the OR example changes. |
examples/plot_optic_radiations.py
Outdated
|
|
||
| if len(aus.SegmentedSFT.fromfile( | ||
| my_afq.export("clean_bundles")["NDARAA948VFH"]).get_bundle( | ||
| "L_OR").streamlines) > 1: | ||
| montages = my_afq.montage("L_OR", (1, 1), "Axial") | ||
| my_afq.combine_bundle("L_OR") |
There was a problem hiding this comment.
@36000 : why is combine_bundle called here? At this point, the image has presumably already been created.
There was a problem hiding this comment.
This is a smoke test for that function. It's the only place it is called. It could probably be moved into it's own, more comprehensive test using example streamlines but it would not be trivial, as it is attached and enmeshed with the GroupAFQ object.
There was a problem hiding this comment.
I'd rather not include this test here. I think that the examples should primarily serve as guidance for users getting acquainted with the software. Admittedly, we need to do some work in some of the other examples, to move them in that direction.
Hope this makes it so that the montage gets displayed.
No description provided.