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Notes:
Changes:
CONN14p change log:
Cumulative patch, bug fixes and improvements
Cumulative CONN14 change log:
Ver Change
__________________________________________________________________________________________________________________________________________
14 Added surface-based analyses
freesurfer compatibility
surface support for spatial voxel-to-voxel measures
permutation analyses for cluster-level stats
GUI support
(*) Modified BA.img Brodmann areas atlas (Lancaster transform to
improve MNI coregistration)
(note: to replicate results analyzed in previous versions select
original BA.img file)
Improved 3d rendering displays & options
Added option "frequency filter" to 1st-level analysis (estimates
spectral decomposition of seed-to-voxel and ROI-to-ROI
connectivity)
Added option "condition-specific frequency filter" to
Setup.Conditions (to analyze frequency-dependency of fcMRI
measures)
14.f Cumulative patch fixing GUI error conditions
Added ability to run individual spatial-preprocessing steps on
structural/functional files (Tools.SpatialPreprocessing GUI menu)
14.g Cumulative patch fixing GUI error conditions
Added subject-sorting uicontext menu to Tools.Calculator display
(*) Added option to apply despiking before or after regression
step; change default setting to 'after regression' (deprecated
despiking effect in favor of ART-based scrubbing)
(note: to replicate results analyzed in previous versions change
value to 'before regression');
Added ability to run arbitrary sequences of multiple spatial
preprocessing steps to Tools.SpatialPreprocesing
Changes to the default spatial preprocessing pipeline
Added defaultMNI (for MNI-space volume-based analyses) and
defaultSS (for subject-space surface-based analyses) default
preprocessing pipelines to preprocessing wizard and
Tools.SpatialPreprocessing
(*) Change realign to realign&unwarp in the default spatial
preprocessing pipeline (for additional control of motion-related
effects)
(note: to replicate results analyzed in previous versions select
select 'other', enter 'default MNI pipeline', and change
'functional Realignment & unwarp' to 'functional Realignment')
(*) Added ART outlier detection & scrubbing as part of the default
spatial preprocessing pipeline (for additional control of
motion-related and other BOLD signal artifacts)
(note: to replicate results analyzed in previous versions select
select 'other', enter 'default MNI pipeline', and remove
'functional Outlier detection (ART-based scrubbing)' from the
selected list of spatial preprocessing steps)
(*) Removed slice timing correction in the default spatial
preprocessing pipeline (to minimize the impact of potential outlier
scans in conjunction with ART)
(note: to replicate results analyzed in previous versions select
select 'other', enter 'default MNI pipeline', and add 'functional
Slice-timing correction' as the first step in the spatial
preprocessing list)
14.h Improve 'explore clusters' bar display (clearer
labels/ordering)
GUI 'Setup->2nd-level covariates' added ability to define new
covariate as a function of other existing covariates (e.g. easily
defining modulation/product terms)
(*) Added a detrending regressor when selecting 'Regress out
covariates' for PCA decomposition of multi-dimensional ROI signal
(note: to replicate results analyzed in previous versions change
'DETRENDBEFOREPCA=true' to 'DETRENDBEFOREPCA=false' in
conn_process.m)
Additional samples of preprocessing pipelines added to
Spatial.Preprocessing menu (e.g. using phase correction when VDM
files are available)
Added the possibility to define subject-specific TR values
14.i Cumulative patch fixing several error conditions
Spatial preprocessing steps are always prompted for user
confirmation (except batch processes) to increase awareness of the
choice of spatial preprocesing options and to give users a better
chance to adapt these to their needs
Added slice timing correction back to the spatial preprocessing
pipeline templates (reverted change introduced in 14.g to maintain
consistent behavior with previous versions and until clearer
community consensus is reached on this issue; users may consider
removing this step for relatively small TR values; Changwei W. Wu
et al. (2011) Empirical evaluations of slice-timing, smoothing, and
normalization effects in seed-based, resting-state functional
magnetic resonance imaging analyses; Smith et al. (2013)
Resting-state fMRI in the Human Connectome Project)
Added options for polynomial detrending (linear/quadratic/cubic)
during Preprocessing step
Added 'Removal of initial scans' to list of optional spatial
preprocessing steps (this step allows users to easily drop the
first few scans in each session from the analyses)
Added new first-level analysis option (for ROI-to-ROI and
seed-to-voxel analyses) : standard PsychoPhysiological Interaction
(PPI) analyses of task-related effects as well as
PhysioPhysiological Interactions (note: FSL-style implementation,
where task-effect interaction factors are hrf-convolved and linear
interactions are modeled on the resulting BOLD-level signal; c.f.
SPM-style implementation which deconvolves the BOLD timeseries
instead and interactions are modeled on the resulting
"neural"-level signal)
Added option for defining arbitrary temporal-modulation factors in
Setup.Conditions and perform PPI analyses of these factors
(pre-requisite for dynamic connectivity analyses)
Preprocessing step output files have been reorganized to avoid
duplication in the presence of multiple conditions (save storage
space / processing time; note: as a consequence when selecting
'Create confound-corrected time-series' now only one nifti file
will be created per subject -containing the entire timeseries-
instead of one file per condition as before -containing each only
those scans/samples associated with each condition-)
Added option in seed-to-voxel results explorer to specify T-value
voxel-level thresholds (note: limited-precision of associated
voxel-level p-values makes using T/F-value thresholds useful when
you wish to threshold very strong effects; e.g. p<1e-10)
14.j (internal distribution only)
14.k Cumulative patch fixing error conditions
Added option for sliding-window temporal decomposition of FC
measures (in Setup.Conditions.TimeFrequencyDecomposition)
Added ability to re-run Setup/Preprocessing steps for only a subset
of analysis types (ROI-to-ROI/Seed-to-Voxel/Voxel-to-Voxel;
user-selection when pressing 'Done')
Added ability to re-run Preprocessing/FirstLevelAnalysis steps for
only a subset of conditions (user-selection when pressing 'Done')
Added ability to use ROIs defined in fsaverage-space (e.g. from
surface-based result masks, or surface-based parcellations) (only
available when selecting structural volumes that have been
processed in FreeSurfer)
Cumulative GUI updates (less cluttered GUI layout and more detailed
help tips throughout main CONN gui (e.g. right-click on data files
to access data folders; easier access to and higher user-control of
the display options in the "ROI-to-ROI results explorer")
Added "structural/functional manual orientation" to the list of
potential spatial preprocessing steps (centers, rotates, reflects
structural/functional volumes, typically to bring these closer to
templates prior to coregistration/normalization)
Cumulative patch fixing compatibility issues with SPM12b
(*) Added support for new SPM12 normalization and segmentation
spatial preprocessing steps (new methods only available when using
SPM12)
(note: to keep using the older normalization/segmentation
procedures under SPM12 set the variable "PREFERSPM8OVERSPM12=true"
in conn_setup_preproc.m)
Added Dynamic Functional Connectivity analyses
"First-level Dynamic FC" estimates data-driven temporal-modulation
factors that characterize the observed dynamic changes in
functional connectivity (ROI-to-ROI connectivity matrix from
selected ROIs)
The resulting factors are entered into standard PPI analyses to
characterize dynamic changes in FC
Additional Seed-to-voxel or ROI-to-ROI analyses (for the selected
or other ROIs) can be computed by selecting "temporal modulation
effects (Dynamic FC)" in the first-level analysis "analysis type"
option.
Aggregated subject/condition measures are also computed to analyze
between-subject/condition differences in temporal modulation
strength for each factor
Added new sample ROI files to conn/utils/otherrois/ ("large-voxel"
MNI-space ROI parcellations covering grey-matter areas; P###.img;
###=number of ROIs from P304.img -20mm ROIs- to P2186.img -10mm
ROIs-)
14.l Cumulative patch fixing GUI error conditions (includig
window-resizing and java-related-errors in some older Matlab
versions)
Cumulative patch fixing Preprocessing issues (completed batch
commands for flexible preprocessing pipeline; added "interleaved
(Siemens)" and fixed prompt for sliceorder (asking sliceorder for
each subject) in slice-timing preprocessing step; Added prompt for
user-defined ART-thresholds in ART preprocessing step; included
centering prior to structural segmentation or normalization like
previous versions; fixed error-reporting problem in preprocessing
steps (errors occuring inside spm batch processes were not being
appropriately captured/displayed by CONN error-handling routines);
remove art_mask_temporalfiles* after art preprocessing step)
14.m (internal distribution only; CONN course)
14.n Cumulative patch fixing error conditions
(*) Default Denoising steps set to "no despiking" (deprecated
despiking effect in favor of ART-based scrubbing)
(note: to replicate analyses in previous versions change to
"despiking (after regression)")
14.o Cumulative patch, bug fixes and improvements
GUI changes (reduce clutter, more detailed help, early warnings on
incomplete Setup information, more-responsive gui, fix Mac issues,
some Matlab 2014b issues, light- and dark- background support)
Reorganize Dynamic FC analysis output into Dynamic scores
(average/baseline and variability/modulation-strength of observed
temporal modulation factors) and Dynamic loadings (ROI-to-ROI
connectivity matrices characterizing modulations in functional
connectivity)
Added new default atlas (132 ROIs) combining FSL Harvard-Oxford
atlas cortical & subcortical areas and AAL atlas cerebellar areas
(see conn/rois/atlas.info for details), as well as collapsed ROI
file with MPFC/PCC/LLP/RLP Fox ROIs (see conn/rois/dmn.info)
Added to second-level results explorer a new "Slice display" option
(display analysis results on individual slices)
Facilitate post-hoc seed-to-voxel analyses by adding to
"second-level results explorer import values&explore values"
options the ability to use alternative cluster-definition files
and/or to extract connectivity values from alternative second-level
analyses (e.g. estimate current-analysis effects within
alternative-analysis clusters, or alternative-analysis effects
within current-analysis clusters)
Facilitate longitudinal studies by adding the possibility to
specify session-specific anatomical volumes (different anatomical
volumes across sessions) as well as session-specific ROIs
(different ROI files across sessions, e.g. gray/white/CSF masks
generated when using session-specific anatomical files)
More flexible SPM import functionality by adding the possibility to
specify session-specific SPM.mat files when importing experiment
information from SPM
Added red/blue colormaps & colorbars for the display of two-sided
results in "surface display", "volume display", and "slice display"
in second-level results explorer
14.p Cumulative patch, bug fixes and improvements
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