[Neuroimaging] Upcoming nibabel bug fix release

Ben Cipollini bcipolli at ucsd.edu
Mon Nov 9 08:13:47 EST 2015

Hi David,

CIFTI support is not complete in nibabel, so no way to do it in nibabel yet.

Have you tried using the conversion tools inside of Connectome Workbench?
Have you tried asking about the fieldtrip issue on the HCP email list? They
tend to be very responsive.


On Mon, Nov 9, 2015 at 2:48 AM, David Dalmazzo <davmazo at gmail.com> wrote:

> Hi all,
> Sound that new python version is not totally compatible with nibabel. My
> question is, it is possible to parse Cifti files from HCP using older
> version of Python? I found very complicated to resolve this task of extract
> connectome data from those files, not even with Matlab R2015b
> ( library fieldtrip is not working properly.
> Someone has a different technique to extract connectome matrix from
> .dconn.nii files?
> Thanks
> David
> On Sun, Nov 8, 2015 at 3:43 PM, Christopher J Markiewicz <effigies at bu.edu>
> wrote:
>> Hi all,
>> Python 3.5, numpy 1.10, and the upcoming pydicom 1.0 are all taking the
>> opportunity to break nibabel in little ways, so it seems like a good
>> time to push out a bug-fix release (v2.0.2).
>> Since 2.0.1, a lot of effort has gone into rearchitecting, and we (by
>> which I mostly mean Ben Cipollini) are plugging along toward cleanly
>> integrated Gifti and Cifti support. For simplicity, I'll be leaving that
>> work out of the current release so that all of the relevant changes can
>> be released at once.
>> I'm doing the preparation work for 2.0.2 in GitHub issue 377
>> (https://github.com/nipy/nibabel/pull/377), so I'd appreciate as many
>> eyes on it as can be spared. In particular, if there's a bug fix that
>> I've failed to include, or if you have a bug to report, please let us
>> know.
>> There is one outstanding bug - breaking the Python 2.7 build on 32-bit
>> Windows - that I would like to resolve before release, if anybody has
>> thoughts: https://github.com/nipy/nibabel/pull/367
>> Thanks!
>> --
>> Christopher J Markiewicz
>> Ph.D. Candidate, Quantitative Neuroscience Laboratory
>> Boston University
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