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###Overview The neuroimaging analysis kit (NIAK) is a library of functions for the preprocessing and mining of large functional neuroimaging data, using GNU Octave or Matlab(r). Essential documentation can be found on the NIAK website: http://www.nitrc.org/projects/niak

###Contributors The NIAK is developed and maintained by members and collaborators of the SIMEXP laboratory, Department of Computer Science and Operations research (DIRO), Geriatric institute of Montreal (CRIUGM), University of Montreal. Many of the functions of the kit are based on software developed over the years by members and collaborators of the Brain Imaging Center, McGill University. See the contributors page for more details.

###News

####August, 23rd, 2013 Release of NIAK 0.7.1 "ammo". This is an update on the 0.7.0 release where the version of PSOM (1.0.1) had a bug in the update feature. See the [http://code.google.com/p/niak/wiki/ReleaseNotes release notes] for details.

####August, 17th, 2013 Release of NIAK 0.7 "ammo". Main features:

• A new pipeline for region growing. This can be used to generate a functional brain parcellation, controlling 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.

####January, 19th, 2011 There will be a poster presentation (#4301) on NIAK at the Human Brain Mapping conference in Québec City, Canada, June 26th-30th 2011.

####January, 17th, 2011 Release of NIAK version 0.6.4.1. Mainly a bug-fix release. Main features :

• Bug fix in the fMRI preprocessing pipeline : the option to get rid of volumes in the motion correction corrupted the data (opt.motion_correction.suppress_vol).
• Bug fix in the fMRI preprocessing pipeline : with multi-session data, the average fMRI volumes are off. As a result, the fMRI to T1 coregistration was likely to fail.
• The pipeline manager (PSOM) is now much faster to initialize and submit jobs. See the release notes for details.

####December, 7th, 2010 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 release notes for details.

####November, 30th, 2010 A new version of NIAK (0.6.3.4) has been released for testing purposes. There are major bugs in this major update, which will soon be replaced by a stable release.

####October, 26th, 2010 Today, the full fMRI preprocessing ran successfully in Octave for the first time. This is opening a new world of perspectives for parallel analysis in massive supercomputing environments.

####October, 8th, 2010 Revision 1000 of the subversion repository was commited today. Happy revision-day Mr NIAK !

####May, 21st, 2010 Release of NIAK version 0.6.3 :

• The main new feature is the way temporary file names are handled. In the old system, it was possible that two jobs running on the same machine ended up using the same temporary file names, resulting into conflict and crash. That should not happen anymore.
• Deleting the "PIPE.lock" file in the logs folder will now force the pipeline manager to stop, even if it is running in the background.
• There have been a lot of improvements/development towards an improved preprocessing pipeline and an fMRIstat pipeline, but nothing complete yet. See the release notes for details.

####January, 15th, 2010 Release of NIAK version 0.6.2. There are new tools for General Linear Model (GLM) analysis, but no pipeline (yet). The main functions of the fMRIstat package of K. Worsley have now been "NIAKified". This is an important intermediate step towards release 0.7. See the release notes for details.

####March, 25th, 2009 There is now a PDF presentation of the NIAK tools and in particular the fMRI preprocessing pipeline.

####February, 1st, 2009 Release of NIAK version 0.6. A slight change in the roadmap of the project explains the absence of version 0.5. The main new feature is that the pipeline system has been redesigned and turned into an independent project called [http://code.google.com/p/psom/ psom]. Running pipelines in NIAK is now much more straightforward than it was in version 0.4. PSOM is distributed inside the NIAK package and the user's guide has been updated.

####November, 27th, 2008 Adaptation of a NIAK logo from an original work by the artist [http://mattahan.deviantart.com/ Mattahan] under a [http://creativecommons.org/licenses/by-nc-sa/3.0/ creative commons license].

####September, 12th, 2008 Release of NIAK version 0.4. The main new feature is the CORSICA method to correct for physiological noise that have been added to the pre-processing of fMRI data.

• New bricks include individual spatial ICA (and PCA), selection of ICA components based on spatial priors, and suppression of ICA components
• A specific template for physiological noise correction.

####September, 2nd, 2008 There is now an online user's guide to the project. It is available on the McConnell Brain imaging center (BIC)'s [http://wiki.bic.mni.mcgill.ca/index.php/NeuroImagingAnalysisKit wiki].

####May, 21st, 2008 Release of NIAK version 0.3. The main new feature is a versatile pipeline for fMRI pre-processing :

• Multiple pipeline styles available, optimized for linear modeling or connectivity analysis.
• Available bricks include : slice-timing and motion correction, spatial and temporal filtering, coregistration between T1 and T2 images, linear and non-linear fit in the MNI stereotaxic space with optional resampling of fMRI data in this space.

####March 7th, 2008 The first public release (0.2) is now available for download, which features :

• reader/writer for MINC1, MINC2, NIFTI and ANALYZE files
• the pipeline system
• A few bricks for fMRI data preprocessing (slice timing, spatial smoothing, temporal filtering).