John Kruper
John Kruper
This looks good. I am going to make export_all vs export("profiles") a choice in the json.
PyAFQ docs need to be updated, because it can be a string in the case of participantAFQ . I will debug this further when I get back from OHBM on...
If you look at the trk files in the pyAFQ output directory, is there one with the name "model-XXX_desc-XXX_tractography.trk" ? Or is it just one named "model-XXX_desc-XXX-AFQ_tractography.trk" ?
This means it is using an imported tractography from qsiprep. This means 1 of 2 things is happening: (1) it is somehow using a different or wrong trk produced by...
After double checking the mapping results I think the problem is there. You can see this in your own dataset comparing template_xform to b0. I will let you know when...
I have a similar issue, and would be willing to help update the code if needed
@araikes sorry for the delay in responding to this. @araikes or @margokersey , I think this issue may be fixed in #533 . Could you try building a qsiprep docker...
I believe this is not an issue anymore. pyAFQ can be run like the other reconstruction pipelines shown here: https://qsiprep.readthedocs.io/en/latest/reconstruction.html . I am going to try to get this issue...
@mattcieslak can you close this issue?
The same change should be made to this file: https://github.com/PennLINC/qsiprep/blob/master/qsiprep/data/pipelines/mrtrix_multishell_msmt_pyafq_tractometry.json