Contact Mark Jenkinson about matlab interface for nifti

[hjmjohnson]

• Mark generated the first variation of the matlab nifti file reading capabilities. This may have updates in the FSL code.

[hjmjohnson]

Hello Mark, John, Michael,

Hans Johnson (cc'd) contacted Rick (cc'd) and me about the SourceForge site
for the niftilib project (http://niftilib.sourceforge.net/).
He is interested in porting it to github for better integration with ITK. As he
points out, this is timely as SourceForge has discontinued support for the cvs
repo system we had been using, and, in general the site has not been updated
in years. We would need to port to svn on SF, or, could take this opportunity
to migrate to github.

Rick and I both have no objections to moving niftilib to github. Especially since
Hans has volunteered to do the migration work (see below for test sites he has already set up).
Quick questions for you are:

1. Are you OK with us moving your niftilib code as is to github ?
2. Do you have preference as to how exactly the repo(s) are structured on github (more detail below) ?
3. Michael, we are thinking that perhaps the PyNIfTI code can now be dropped, and we just retain your
   notice and link indicating that PyNIfTI has been superceded by nibabel. But we are happy to go with
   what ever you think is best on this.
4. John, Hans is suggesting we consider pointing folks to the newer spm12 code at your FIL site, what do you think ?

Hans and Rick and I had a zoom meeting to discuss, we are happy to set up a meeting w/ you or to
discuss/finalize via email. Hans is quite anxious to move swiftly on this, I think he has a window of
time over winter break to work on this.

As Hans pointed out, the niftilib reference implementation has for the most part not been updated in close
to a decade. Been awhile since I've been in touch w/ you, hope all is going well with everyone.
I have seen your new releases come out !

More details on the proposed github setup below. If you send us github ids we can add
you to the projects.

best,
Kate

----- github details ---------------

One question is whether we create 1 repo with folders for C, Java, Matlab, Python (if we keep it)
implementations, or, if we make 3 separate repos. Hans set up both options for us to look at:

One repo: niftilibs

Three repos: nifti_clib nifti_java nifti_matlab

It seems clear that in any case the niftilib documentation is best moved to a separate
repo and Hans has set that up as NIFTI-Imaging.github.io

Hans is in favor of 3 separate repositories because the matlab code is under a different license than Java or C and he
feels mixing licenses within a repo is difficult for others to incorporate. Also, he feels keeping the nifti_clib as a
self-contained repository will make upstream integrations (i.e. ITK, afni, and the distribution package management
systems like Debian) cleaner. I think Rick and I do not feel strongly one way or the other about this, aside from that I think
it would be good to keep a strong connection between the implementations.

Another question is what github organization the repo(s) be placed in. We discussed making
a new organization, and Hans set that up as NIFTI-Imaging, (NIFTI was taken) and we discussed potentially
adding the repo(s) to the ITK or some other organization. Pls let us know if you feel strongly as to what
github organization this would go in.

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