[MINC-users] NIAK release 0.6.4

[Pierre Bellec]

Dear Minc users,

I am happy to announce the release of NIAK 0.6.4 (beta). This is a major
update in terms of both design and dependencies. The main features are now
:
* Full compatibility with Octave and Matlab for Linux. MINC1 and MINC2 file
formats are supported.
* A single dependency on the opensource project called MINC tools
http://en.wikibooks.org/wiki/MINC
* Reader/writer for MINC.
* An fMRI preprocessing pipeline. Highlights : non-linear fit of the
structural image in stereotaxic space (CIVET-like) and correction of
physiological noise based on ICA (CORSICA).
* All the tools used by the pipeline are also available as flexible modules
using a consistent syntax.
* Powerful pipeline capabilities, including parallel computing, generation
of detailed logs and automatic management of pipeline failures or updates.

Note that NIAK 0.6.4 has been installed at the "Unité de Neuroimagerie
fonctionnelle", "Centre de recherche de l'institut de gériatrie de Montréal"
as well as on the "Brain imaging center", "Montreal Neurological Institute".
Site-specific instructions can be found
here<http://www.nitrc.org/plugins/mwiki/index.php/niak:Installation#Site-specific_installations>.
The installation at the BIC now uses the linux-64 bits queue, and the MINC2
package found in /usr/local/bic. This should hopefully limit or even
suppress the errors that happened from time to time so far on all.q.

The main changes between 0.6.4 and 0.6.3 are :
* A new version of the user's
guide<http://www.nitrc.org/frs/downloadlink.php/2726> 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. Regarding
this pipeline :
  * 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 <http://code.google.com/p/niak/wiki/ReleaseNotes> for
details. The new release can be downloaded
here<http://www.nitrc.org/frs/downloadlink.php/2728>.
There is also a new
website<http://www.nitrc.org/plugins/mwiki/index.php/niak:MainPage>
 with installation<http://www.nitrc.org/plugins/mwiki/index.php/niak:Installation>
instructions
and a tutorial<http://www.nitrc.org/plugins/mwiki/index.php/niak:FmriPreprocessing>
for
the fMRI preprocessing pipeline.

Watch out for the next 0.7 release, featuring a full multi-level linear
model pipeline based on a NIAKified version of fMRIstat.

Best regards,

Pierre Bellec, PhD
Chercheur adjoint
Centre de recherche de l'institut de Gériatrie de Montréal
Département d'informatique et de recherche opérationnelle
Université de Montréal
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
(001)(514) 340 3540 #336730