Slf123new

[jyeatman]

added SLF 1/2/3
@arokem will you update this with files on figshare?

[arokem]

Looks great! A couple of thoughts: I think that it is helpful to show users how to download some ROIs to a well-defined location in their file system and operate with these files. I think this example achieves that well. That said, I think that we will also want something a bit more automatic to do when we are running code to find these different SLF sub-segments in real use-cases, because I don't think we'll want to copy and paste all those paths into our scripts. So, I do think that we'll want to implement some convenience functions for working with these ROIs, in addition to this example. Something along the lines of this suggestion on the cerebellar peduncles PR. WDYT?

[jyeatman]

@arokem I totally agree. Can you help with this? To summarize:

• we should implement some helper functions that go in the main code base to make this segmentation a default like VOF is.
• in this tutorial we can include commented out versions of those helper functions but keep the full tutorial for teaching sake but also referring to the "correct way"

@36000 the visualization code at the end crashed with the following error. Also, the montage just had renderings of an axial view in individual subjects with no montage combining them. Also, I want these for all the pathways not just one. Can you help?

Traceback (most recent call last):
File "/Users/jyeatman/git/pyAFQ/examples/tutorial_examples/Add_Custom_Bundle.py", line 189, in
#############################################################################
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'L_SLF1'

[jyeatman]

@arokem @36000 I think this is ready to merge. I would like the example to show the montage figures and also have the interactive HTML for 2 subjects. Would that work?

[arokem]

This is great! Some suggestions and comments below.

[arokem]

Maybe we should explain what's going on here?

[arokem]

Emphasizing perhaps that these ROIs can be files that the user created themselves, but that in this case they are simply files stored somewhere on the internet (which happens to be another software library with a very similar name - this could get confusing for someone who doesn't know all the history...)

[jyeatman]

@arokem I just added this. Please edit as you see fit and I'll merge

[arokem]

I've done another round of editing some of the text and formatting in the examples. I believe this is ready to merge, so I will go ahead with it. If we need to do more fixes, we can follow up on a separate pr.