This release corresponds to NIAK version 1887 and PSOM version 760
(release 1.0.2), as numbered by the subversion repository. Main
* 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
* The default of FLAG_NU_CORRECT in the slice timing brick was
also set to off, because for a reason that is unknown at this time
this operation behaves differently on different computational
platforms. With default parameters, the three pipelines released as
part of NIAK 0.7.1 have been successfully tested for
reproducibility on two different computational platforms (Ubuntu
12.04 vs CentOS 5.5, both with Octave 3.6.2 and minc-toolkit
0.3.18). The tests were performed both within and between
* Lots of other minor features and bug fixes.
* New pipeline to generate graph properties on connectomes and
functional connectivity maps (niak_pipeline_connectome). The graph
measures are based on the brain connectivity toolbox https://sites.google.com/site/bctnet/
* New pipeline for region growing
* a command for region growing in 3D (niak_region_growing)
* a new brick for region growing on a single subject's fMRI
* a new pipeline for region growing with multiple fMRI datasets
* New tools for linear model analysis:
* read a model in CSV format (niak_read_model)
* least-square estimation (niak_lse)
* general linear model analysis (niak_glm)
* "normalization" of a model, i.e. orthogonalize, correct for
mean/variance, create interaction terms, select subsects of the
data, etc. (niak_normalize_model).
* White's test for heteroskedasticity (niak_white_test_hetero)
* New statistical tools
* bootstrap of time series (niak_bootstrap_tseries)
* false-discovery rate in a family of p values (niak_fdr)
* New tools for clustering:
* hierarchical clustering (niak_hierarchical_clustering)
* threshold a hierarchy (niak_threshold_hierarchy)
* re-order points based on a hierarchy (niak_hier2order)
* re-order points based on a similarity matrix and a partition
* visualize a hierarchy (niak_dendrogram)
* visualize a partition (niak_visu_part).
* An improved version of k-means clustering (with bisecting
approach, k-means++ initialization, optimized code, and others)
* Surface analysis:
* A new reader for surface data (niak_read_surf)
* A new tool to visualize surface data (niak_visu_surf)
* New surface template
* A new brick to interpolate volumetric data on the surface
* fMRI preprocessing:
* Added the scrubbing method of Power 2012
* Preprocessed file now have a xxxx_extra.mat companion, including
all confounds that have been regressed out as well as a list of
* Added some regression of confounds in the pipeline
* Added a correction of the global average "à la Carbonell" in
* Added the COMPCOR method to correct structured noise in fMRI
* the CORSICA method is now off by default
* The default resolution for the normalized fMRI datasets resampled
in stereotaxic space is now 3 mm isotropic.
* It is now possible to choose between the symmetric (default) and
asymmetric MNI brain templates for coregistration of T1 scans in
* lots of new measures for quality control
* A new tool to estimate partial volume effects on a T1 volume
(thanks to Jussi Tohka, niak_brick_pve)
* A new version of the AAL parcellation, tweaked to fit the
non-linear symmetric MNI template (40 iterations).
* A new "grabber", i.e. a function to parse the outputs of the fMRI
preprocessing pipeline, select a subset of QCed subjects, and
generate a structure that can be fed in other pipelines such as the
region growing pipeline (niak_grab_fmri_preprocess).
* Many bug fixes and minor improvements.