NeuroImaging Analysis Kit (NIAK) News

"ammo" NIAK 0.7

Pierre Bellec — Wed, 09 Apr 2014 2:53:17 GMT

A bit of late announcement: "ammo" NIAK 0.7 was released in 2013. Main features:
* A new pipeline for region growing. This can be used to generate a functional brain parcellation, co ntrolling for the regions' size and/or homogeneity, at the level of an individual or a group. Methods as described in Bellec et al., Neuroimage 2006.
* A new pipeline to generate connectomes, functional connectivity maps as well as graph properties. This pipeline depends on the brain connectivity toolbox.
* A revamp of the fMRI preprocessing pipeline. Now includes regression of average signals in the ventricles and the white matter, scrubbing, regression of the global signal "a la Carbonell", regression of the motion parameters after PCA reduction, COMPCOR, symmetric or asymmetric MNI brain template, and other goodies.
* Lots of other minor features and bug fixes.

See the release notes for details:
https://code.google.com/p/niak/wiki/ReleaseNotes

NIAK@HBM

Pierre Bellec — Sun, 19 Jun 2011 4:57:28 GMT

There will be a poster presentation (#4301) on NIAK at the Human Brain Mapping conference in Québec City, Canada, June 26th-30th 2011.

NIAK release 0.6.4.1

Pierre Bellec — Mon, 17 Jan 2011 9:12:53 GMT

Release of NIAK version 0.6.4.1. This is mainly a bug-fix release for the fMRI preprocessing pipeline :
* the option to get rid of volumes in the motion correction corrupted the data (opt.motion_correction.suppress_vol). If the number of suppressed volumes was zero (which should be the case with any dataset acquired recently) there was no problem.
* with multi-session data (i.e. two or more than two fields "session1", "session2" etc were used), the average fMRI volumes are off. As a result, the fMRI to T1 coregistration was likely to fail.
Also, the pipeline manager (PSOM) is now much faster to initialize and submit jobs.
See the [http://code.google.com/p/niak/wiki/ReleaseNotes release notes] for details.

NIAK release 0.6.4

Pierre Bellec — Wed, 08 Dec 2010 3:09:45 GMT

Release of NIAK version 0.6.4. Main features :
* NIAK is fully compatible with Octave.
* NIAK only depends on the opensource project called the MINC tools http://en.wikibooks.org/wiki/MINC
* A new version of the user's guide in PDF. This guide applies as of NIAK release 0.6.3.4.
* A completely revised fMRI preprocessing pipeline. Scripts written for the old system should still work, but it would be better to update the script to conform to the new template. This will require minimal effots. Main changes :
* There are no "styles" anymore. Most steps of the pipeline can instead be skipped using dedicated flags making the whole flowchart flexible.
* There are lots of new steps for quality control purposes.
* The T1-fMRI coregistration should work better.
* The parameters of the slice timing correction are much more straightforward to specify.
* the motion correction operates at the run level if possible, and is much faster. The strategy is also now fully hierarchical : within-run, between-run within-session, between-sessions.
See the [http://code.google.com/p/niak/wiki/ReleaseNotes release notes] for details.

New updated user's guide 0.6.4

Pierre Bellec — Tue, 07 Dec 2010 7:39:41 GMT

A new PDF overview of NIAK has just been released. It covers all the new features of NIAK 0.6.4.

NIAK goes NITRC !

Pierre Bellec — Tue, 23 Nov 2010 7:09:08 GMT

The main NIAK site is now on NITRC. The site is still very incomplete, but the essential documentation can be found on the wiki.