CONN change log:
Ver Change
22.u2407
Cumulative patch,
bug fixes and improvements
Added ''''New
(download)'''' option to Projects menu, to create a new CONN
project by downloading and automatically preprocessing and
denoising publicly available datasets from FCP/INDI
repository
Added ''''polar
display'''' options to results explorer GUI (showing the
"location"/overlap of each cluster with respect to the 7 canonical
networks in Yeo&Buckner2011)
Reorganized
''''other imaging data'''' tab in GUI to make its use simpler /
more intuitive
(*) Added options
to gPPI first-level analyses to output a measure of
"connectivity-change" (regressor coefficient associated with
physiological interaction term in gPPI model) or "total
connectivity" (sum of regressor coefficients associated with
physiological and physiological-interaction terms in the same gPPI
model)
note: already
existing analyses are unchanged, and if/when they are re-run they
will still use the same settings as they had originally
(''''connectivity-change'''' option)
new gPPI analyses
will be defined by default with the ''''total-connectivity''''
option. To create a new analysis using the same options as in the
previous versions simply change the option to read
''''connectivity-change'''' instead
Added
QC_OutlierSubject and QC_ValidSubjects quality control variables
created during QC_Variables plot (marking subjects with extreme
outliers in any of the selected QC variables)
Added
ExcludeOutlierSubjects second-level covariate (automatically
created from QC_OutlierSubjects) and which can be direclty added to
any 2nd-level analysis as a standard control variable when wishing
to exclude all outlier subjects from this analysis
Added
''''functional_sliceintensity'''' preprocessing step correcting
slice intensity differences (e.g. for sparse acquisition sequences,
where scanner transients cause differences in intensity across
slices / banding)
Added pointers
(saved as secondary datasets) to original structural data in
preprocessing pipeline
Added option in
invPPI to specify hanning window length
Added QC plot
creation to conn_repositories (preprocessing pipeline applied to
all FCP/INDI downloads)
Added
conn_polar_display for displaying the breakdown/overlap of a
mask/cluster into different networks (networks defined from
Yeo&Buckner 2011 7-network parcellation)
Added
Buckner2011.nii parcellation to util/otherrois (containing Buckner
cerebellar parcellation into Yeo 2011 7-network areas)
Added option to
select multiple BIDS/fMRIPrep folders when importing data into a
CONN project
Added
''''structural_label_as'''' and ''''structural_load_from'''' steps
during preprocessing to save/load state of structural images to
secondary datasets
Changed the
default MNI pipeline to generate new additional secondary datasets
labeled ''''original structural images'''' and ''''mnispace
structural images'''' containing the corresponding subject-space
and mni-space structural images
Added GUI options
in the Setup.functional and Setup.structural tabs to easily move
different states of structural and functional data from/to
secondary datasets
Added automatic
import of participants demographic data when downloading and
processing FCP/INDI datasets
Added
conn_repositories to access and download data from FCP/INDI
repository
(*) Changed
functional centering in default MNI pipeline to be applied before
realignment (this helps in datasets that have excessive motion
between runs/sessions)
note: if you
prefer to run the previous-version default MNI pipeline (with
centering applied after realignment), in the preprocessing window
click on ''''load'''' and select the pipeline
''''defaultMNI_legacy2023.mat'''' (available in the
conn/utils/preprocessingpipelines folder)
Added
''''realigned data'''' label in default preprocessing pipelines (to
help with visual quality control of realign and SDC steps)
Added ''''public
key'''' authentication option and GUI in ''''connect to remote
projects'''' menu
Initialize
conn_repositories with FC1000 datasets
Added
vdm_fmap_magnitudebeforephase field (default=true) to preprocessing
functional_vdm_create step
Added
XnamesExtended field to .mat file output files from
functional_roiextract preprocessing step
Added
subjectspace preproc pipeline to EL module
Added ''''SSH
using private key authentication'''' method to conn_remotely (e.g.
to connect to AWS nodes)
Allows
batch.Setup.coregsource_functional field to be defined from
''''ref'''' secondary dataset
Added CAT12
neuromorphometrics rois to utils/otherrois
Added shen_268
atlas file in utils/otherrois
Changed new
projects now to start with optional FMAP/VDM/TPM secondary
datasets
Added
''''conn_server_ssh checkcontrolmaster'''' option to remote
connections in order to recreate a missing or timed-out SSH
controlmaster socket when necessary
Added option to
include control covariates (excluding some portion of the
between-subjects variance) in fc-MVPA
Added
gui_colormap option to choose colormap in main GUI
Smoother
transition between slices and additional options in fc-MVPA summary
GUI
Added
multivariate custom-contrast option to fc-MVPA summary gui
Added
conn_batchexample_qcplot (example batch creating QC-FC correlation
plots separately across sites in a study)
previous versions:
__________________________________________________________________________________________________________________________________________
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
15.a Cumulative patch, bug fixes and
improvements
Added more flexible plot-display options to
Calculator
Added selection of colorbar range to
3d-surface results renderings
Facilitate post-hoc ROI-to-ROI analyses by
adding to the "second-level results" tab a barplot display of
individual effects (as well as ''''import values & display
values'''' options, equivalent to those for seed-to-voxel
analyses).
15.b Cumulative patch, bug fixes and
improvements
Added more flexible inputs for ART-based
scrubbing during preprocessing
Added support for slice-timing correction of
multiband sequences (CONN now supports entering "slice timing"
sequence information instead of "slice order")
Added support for subjects with partial
acquisition of condition-specific data (e.g. if a condition has
only been acquired on a subset of subjects, all second-level
analyses involving this condition will automatically be limited to
the subset of subjects with valid condition-specific data; see
Setup.Conditions.MissingData)
15.c Cumulative patch, bug fixes and
improvements
Reorganized and added new options to Dynamic
FC analyses: added display of dynamic factors, display of
ROI-to-ROI connectivity matrix changes across time, display of
dynamic vs. static connectivity measures; added rate-of-change
dynamic measure for each factor
Added support for gPPI models (generalized
PsychoPhysiological Interaction; recommended PPI model to analyze
task-related connectivity in the presence of multiple task
conditions) in addition to sPPI models (single-condition
PsychoPhysiological Interaction)
15.d Cumulative patch, bug fixes and
improvements
Added support for .annot ROI files
(freesurfer parcellation files)
Added display of Denoising voxel-to-voxel
histogram for all subjects/sessions
Added conn_batch_pct function to facilitate
parallel processing of batch commands (see conn_batch_pct.m for
details)
15.e Cumulative patch, bug fixes and
improvements
Added native support in SPM12 of
cluster-level statistics for F-contrasts (when using SPM8 and below
CONN still uses Keith Worsley stat_thresh FMRISTATS implementation
of cluster-level statistics for F-contrasts as in previous CONN
releases)
Added support for SGE (Sun Grid Engine)
parallel batch processing on computer clusters (see help
conn_batch_pct)
Added Second-level covariate
import/export-to-file options (GUI Setup.Covariates tab,
import/export buttons)
15.f Cumulative patch, bug fixes and
improvements
Added fully integrated Grid Engine,
PBS/Torque, and LSF distributed environment parallelization options
for Preprocessing, Setup, Denoising, and Analysis steps (accessible
both through GUI as well as batch commands; see GUI
Help.Documents.GridComputing, Tools.GridSettings, and conn_batch
batch.parallel options)
Facilitate searching through database of
user-community questions/answers from the NITRC Forum by adding
search help functionality to CONN GUI (see GUI Help.Search
menu)
Added batch commands for Preprocessing steps
(same as previous batch.New functionality but it can now be run at
any time, not only when the project was first created; see
conn_batch Setup.preprocessing options)
Added option to import all condition
information from a spreadsheet (in Setup.Conditions ''''condition
tools'''' menu)
Added batch commands for using non-default
Tissue Probability Maps during segmentation/normalization
(SPM8/SPM12) (see conn_batch tpm_template and tpm_ngaus
options)
Added support for .par first-level covariate
files (FSL estimated motion parameters)
Added explicit centering (translation to
(0,0,0) coordinates) of functional and structural data in default
MNI preprocessing pipelines
Added the option to use one-sided (negative)
thresholds for adjacency-matrix generation in graph-theory analyses
(compute graph-measures of anticorrelations networks)
Added option to drop initial scans in ART
(through the GUI and in
batch.Setup.preprocessing.art_thresholds)
Added option to modify the default mask
thresholding value and number of erosion steps for CSF &
WhiteMatter ROI definitions (see conn_batch cwthreshold
field)
15.g Cumulative patch, bug fixes and
improvements
Added ability to compile CONN for use without
a Matlab license or environments
15.h Cumulative patch, bug fixes and
improvements
Added option to extract weighted-sum BOLD
timeseries from ROI files (e.g. for probabilistic ROI definitions,
or dual regression network ROIs)
Added the possibility of defining multiple
functional sets in "Setup.Functional.Functional data for ROI-level
analyses" (to simplify using ROIs in different spaces, e.g. some
ROIs in MNI-space while others in subject-space)
Added support for 4d-nifti ROI atlas files
(one volume per ROI)
Added group-ICA voxel-to-voxel analyses
(spatially independent components using two-step dimensionality
reduction, FastICA for IC estimation, and dual-regression for
subject-level backprojection; see voxel-to-voxel analysis
tab)
Added non-parametric statistics for
voxel-level analyses (residual permutation/randomization tests,
univariate and multivariate models; see Setup.Options "second-level
analyses" field, and "parametric stats/non-parametric stats" option
in results explorer window)
16.a Cumulative patch, bug fixes and
improvements
16.b Cumulative patch, bug fixes and
improvements
Added option to include higher-order power of
confound timeseries (e.g. Friston24 movement parameters)
Added new voxel-to-voxel r-by-distance
scatter plot in Denoising tab
Added ICA display tools, sorting components
(by spatial kurtosis, skewness, spatial correlation with template,
temporal frequency, and temporal variability), and ICA-based
parcellation (''''summary display'''' tab)
Added analyses of variability and frequency
of network timeseries in ICA (''''temporal components''''
tab)
Added analyses of variability and frequency
of modulatory timeseries in dynamic FC (''''temporal components''''
tab)
Added design-display plot in second-level
results tab
Added ability to preview F-contrast and
simultaneously display multiple individual contrasts in
seed-to-voxel second-level results tab
Added multi-slice plots to ''''slice
display'''' gui (in results explorer, and functional/structural/ROI
tools)
Added multi-slice display to ROI-to-ROI
results tab
17.a Cumulative patch, bug fixes and
improvements
Updated manuals/documentation
(*) Changed default ART threshold settings,
when not otherwise defined explicitly they are now set to
''''intermediate'''' (97th percentile: 0.9mm 5sd); previously set
to ''''liberal'''' (99th percentile: 2mm 9sd)
note: if updating mid-analysis and
preprocessing new subjects: define explicitly ART thresholds to
maintain consistency across subjects
(*) Fixed global scaling parameter in
GlobalCorrelation/IntrinsicConnectivity voxel-to-voxel measures
(prior versions computed average correlation coefficient across all
voxels in the volume -with voxels outside of analysis mask set to
0-; new version computes average correlation coefficients across
analysis-voxels only -disregarding voxels outside of analysis
mask-; difference between old and new behavior is a constant
scaling factor for all measures/subjects/conditions equal to
SizeOfMask/SizeOfVolume = 0.2913 for the default analysis mask;
normalized GC/ICC measures not affected by this change)
note: if updating mid-analysis and still
processing new subjects: GlobalCorrelation/IntrinsicConnectivity
voxel-to-voxel analyses that used raw measures (ie. normalization
setting is unchecked) require rerunning all subjects for
consistency
(*) Added ability to define multiple sets of
voxel-to-voxel and dynamic FC analyses within the same conn
project
note: if updating mid-analysis and running
voxel-to-voxel analyses: voxel-to-voxel analyses that defined
multiple measures (e.g. ICA and ICC in the same analysis) are now
to be broken into separate analyses (e.g. one analysis for ICA and
another for ICC); analyses already performed that contain multiple
measures are still supported for back-compatibility but no new such
analyses can be created
Added batch functionality for dynamic FC
analyses
Added new conn/rois/networks.nii atlas with
ROIs characterizing an extended set of classical networks: Default
Mode Network (4 ROIs), SensoriMotor (2 ROIs), Visual (4 ROIs),
Salience / Cingulo-Opercular (7 ROIs), DorsalAttention (4 ROIs),
FrontoParietal / Central Executive (4 ROIs), Language (4 ROIs),
Cerebellar (2 ROIs) (all ROIs defined from CONN''''s ICA analyses
of HCP dataset / 497 subjects)
Added labeling of individual networks in ICA
analyses, and suggestions based on match to ICA template
Added new automatically-generated Quality
Assurance measures: during ART preprocessing and Denoising steps
the following new second-level covariates are now created:
QA_MaxMotion, QA_ValidScans, QA_InvalidScans (maximum inter-scan
motion, number of valid/invalid scans per subject); and QA_GCOR
(global correlation index per subject and condition)
Added script-it option to all
Preprocessing/Setup/Denoising/First-level analyses (for any
analysis step, in addition to running immediately this step CONN
can now also automatically create scripts for the same step to be
run at a later time)
Added masking option for group-level ICA,
PCA, and MVPA analyses (e.g. group-level components in masked-ICA
are restricted to within-mask voxels only; subject-level
backprojection still performed across entire brain /
Setup.AnalysisMask)
Added ''''display single-slice for all
subjects'''' summary displays to structural-/functional-/ROI- tools
(e.g. use to quickly assess correct normalization/coregistration
across all subjects and/or identify outlier
subjects/sessions)
Added ''''Motion-Mask estimation''''
procedure to list of available preprocessing steps (estimating at
each voxel the derivative of the BOLD signal with respect to the 6
motion parameters; when running this preprocessing step MotionMask
ROIs are automatically added to the list of ROIs in Setup.ROIs,
which can then be used during Denoising for additional protection
against motion-related effects)
Added option to separately filter individual
confound effects before denoising regression (equivalent to
''''simult'''' method but allowing control over individual effects;
e.g. filter motion/CompCor regressors but not scrubbing
regressors)
Added connection bundling, display of
reference-slice, user-defined surfaces, and other usability options
to CONN 3d displays
17.b Cumulative patch, bug fixes and
improvements
Added ability to save/share/reuse
user-defined preprocessing pipelines
Added ability to enter DICOM
structural/functional files
Added Quality Assurance displays to visually
inspect the quality of the structural/functional data
coregistration and Denoising step, and easily identify potential
outlier subjects or failed preprocessing steps (see Tools ''''QA
plots'''' option)
Added ALFF/fALFF measures (see Voxel-to-Voxel
first-level analysis tab)
Added ability to bookmark individual
second-level results and plots to help organize complex sets of
analyses and results
Added preprocessing options for indirect
coregistration, explicit direct/indirect normalization, and
realignment without reslicing
Added higher-resolution slice- and glassbrain
displays (see seed-to-voxel or voxel-to-voxel results
explorer)
Added options to display individual-subject
voxel- and ROI-level connectivity measures entered to second-level
analyses (see ''''display values'''' in second-level results
tab)
Added options to import sets of files from a
different CONN project in Setup tab (see ''''AltSelect''''
option)
Added ''''description'''' fields to
second-level covariates (see Setup.Covariates tab), and to
user-defined contrasts (see ''''contrast manager'''' in
second-level results tab)
Added ability to switch between
axial/coronal/sagittal views in Setup tab and ICA results
17.c Cumulative patch, bug fixes and
improvements
Added ability to run preprocessing steps for
individual sessions/runs (this facilitates incrementally adding new
timepoints to an existing CONN project in longitudinal
analyses)
Added QA plots: QA_artifact movie display of
BOLD volumes with ART global/motion/outlier timeseries,
QA_registration plots display original or eroded white/csf
masks
Added option to annotate individual QA
plots
Added QA subject-level measures
QA_MotionMax/Mean and QA_GlobalMax/Mean from ART-derived framewise
motion and BOLD change timeseries
(*) Changed default MNI preprocessing
pipeline (minor changes):
a) moved ART step to be performed before
functional normalization instead of after it (this allows the
functional normalization step to use a mean-functional image
generated by ART which excludes outlier scans, making
coregistration/normalizatoin procedures more robust to the presence
of outliers)
b) changed ''''functional_normalize'''' to
''''functional_segment&normalize'''' (this generates additional
functional gray/white/csf masks to be used in QA plots or as
alternative aCompCor masks)
For back-compatibility or mid-analysis
updates: the exact prior pipeline can be loaded from:
conn/utils/preprocessingpipelines/defaultMNI_legacy.mat
Added compatibility-fix for cluster-computing
options in new SPM+toolboxes standalone ("batteries included"
standalone SPM12 prerelease)
Added GUI options to easily select different
functional, structural, ROI, or first-level covariate files using
filename rules (see ''''reassign all files'''' options in
functional/structural/roi/covariate tools menus)
Added movie displays of functional timeseries
(see ''''display single-slice for all timepoints'''' options in
functional/first-level covariate tools menus, and ''''display
values'''' option in Denoising tab)
Added "art_regression_timeseries*.mat" file
output to ART and associated QA_timeseries 1st-level covariate in
CONN, containing (when using default ART settings) scan-to-scan
changes in global BOLD signal (z-scores), and framewise
displacement timeseries (mm) (timeseries that, when thresholded,
lead to identified outlier scans)
Added "carpet" display of BOLD signal
timeseries to Denoising tab and QA plots (similar to Power et al
2017) to help evaluate the amount of residual whole-brain signals
before and after denoising
Added ability to edit through the GUI and
batch commands the binarization/erosion options for grey matter,
white matter, and CSF masks (see Setup.ROIs.Erosion settings;
previous batch.Setup.cwthreshold field)
Added voxel BOLD signal timeseries display to
GUI (click on brain images on Setup.functionals, Denoising, or
First-level analysis tabs)
Added voxel-level "plot effects", "plot
values", and "import values" menus to Second-level results tab
(click on brain images on Second-level results tab)
17.d (internal conn workshop release)
17.e Cumulative patch, bug fixes and
improvements
Added ability to import condition-information
file using conn_batch commands (see
batch.Setup.conditions.importfile info)
Added ability to load preprocessing-pipeline
file using conn_batch commands (see batch.Setup.preprocessing.steps
info)
Added support for BIDS format *_events.tsv
condition-information files (see Setup.Conditions ''''import
conditions'''' option)
Added ''''roi tools'''' option to create new
spherical-ROI file from user-defined MNI coordinates (see
Setup.ROItools menu)
Additions to parallelization profiles:
User-specific parallelization profiles
(user-specific profiles are now saved in each user folder ~/)
User-defined entries in submitted shell
script (see "in-file" additional submit settings in Tools.Grid/HPC
settings)
Users may now force usage of CONN-standalone
in cluster nodes (see "nodes use pre-compiled CONN only" checkbox
in Tools.Grid/HPC settings)
By default the parallelization GUI will not
query the cluster scheduler for status updates unless explicitly
requested by the user (minimize scheduler load; see "check job
status automatically" checkbox in Tools.Grid/HPC settings)
Stopped ART from displaying GUI when run in
non-interactive mode
Added ability to specify user-defined
activation maps in conn 3d display (see conn 3d display menu
"Surfaces.BrainSurfaces.BrainSurfacesActivation")
Added ability to automatically copy
structural/functional files into local BIDS folder when importing
structural/functional data into CONN (e.g. for use when importing
data from read-only folders) (see "import selected files | copy
first to local BIDS folder" options in Setup.functional and
Setup.structural tabs; see batch.Setup.localcopy field for batch
scripts)
17.f Cumulative patch, bug fixes and
improvements
Additions to parallelization profiles:
Added ability to queue sequential
parallelization jobs (when starting a new parallelization job
through the GUI while another one is still running/pending CONN
will automatically queue this new job; when using batch scrips use
the profile name ''''Null profile'''' to queue jobs)
Simplify operation with queued/pending
parallelization jobs (Tools.ViewPendingJobs will now automatically
detect finished jobs and offer to merge the results or submit the
next set of queued batch jobs)
Additions to standalone release
Compiled with Matlab 2017a (MCR 9.2)
Support for user- and system- level cluster
configuration settings
Support for Environment Modules installation
(see modulefile.txt)
Added alternative Gray/White/CSF
binarization/erosion methods (option to specify binarization
threshold in absolute vs. percentile values; option to specify
erosion kernel size in abolute vs. percentile values; see
''''Erosion settings'''' in Setup.ROIs tab; see batch.erosion
fields for batch scripts)
Added voxelsize_anat and voxelsize_func
separate batch fields for anatomical and functional
normalization/reslicing resolutions during preprocessing (see
Preprocessing GUI; see batch.Setup.preprocessing.voxelsize_*
fields)
Added functional/structural_manualspatialdef
(user-defined non-linear spatial transformations from precomupted
[i]y_*.nii or _seg_sn.mat files) to list of available preprocessing
steps (see Preprocessing GUI; see batch.Setup.preprocessing.steps
for batch scripts)
Added ability to specify slice-timing
information from BIDS-format json files (see Preprocessing GUI; see
Setup.preprocessing.sliceorder field for batch scripts)
Added surface-projection ROI display (see ROI
tools.3d-surface-project viewer)
18.a Cumulative patch, bug fixes and
improvements
Added parallelization profile for Windows 7
and Windows 10 machines
Added ''''pending jobs'''' button to main
CONN gui that alerts when there are running, queued, or pending
jobs in your cluster / HPC environment
Added the ability to parallelize the
computation of permutation/randomization analyses (non-parametric
computation of cluster-level statistics) using Cluster/HPC
jobs
Added QC reports (auto-generated html/pdf/xml
reports containing a user-defined selection of Quality Assurance
plots; see ''''QA plots'''' button or conn_qaplotsexplore from
Matlab command line)
Added QA plots computing QC-FC associations
(association between Quality Control variables and Functional
Connectivity values; see Ciric et al. 2017, NeuroImage,
"Benchmarking of participant-level confound regression strategies
for the control of motion artifact in studies of functional
connectivity")
Added QA plots computing FC vs distance plots
(90% CI of FC r values vs. edge distance (in mm) in a 1000-node
network)
Added QA plots computing histogram /
quartiles / outliers in QC variables (QC second-level
covariates)
(*) Changed preprocessing voxelsize_anat
default value to 1mm (during normalization anatomical volumes are
resampled to 1mm isotropic voxelsize for improved resolution of
anatomical images)
For back-compatibility or mid-analysis
updates please change anatomical resolution to 2mm
Simplified GUI for secondary functional
datasets (secondary dataset-1 and above can now also be defined,
displayed, and preprocessed from the Setup.functionals tab)
Added ''''plot subjects'''' button to S2V and
V2V results tabs, as well as to voxel-level results explorer window
(slice/surface/volume display of individual subject connectivity
maps)
Added ''''export'''' button to ROI-to-ROI
results explorer window (exports suprathreshold connections in
ROI-to-ROI connectivity matrix)
Added interactive thresholding options to
slice display
18.b Cumulative patch, bug fixes and
improvements
Added conn_dcmdir (to display organization of
DICOM files/folders) and conn_dcmconvert (to organize DICOM
files/folders into DICOM series and convert each series to a nifti
file)
Added richer JSON information when importing
DICOM files (including reading RepetitionTime and Siemens
SliceTiming information from DICOM headers)
Added ability to use data with different
TR''''s across sessions/runs (if TR value for a given subject is
set to NaN -e.g. in Setup.Basic tab-, then the TR information will
be read from the ''''RepetitionTime'''' field in a sidecar JSON
file associated with the functional volume, separately for each
subject&session)
Added ''''Import from BIDS dataset'''' GUI to
import CONN Setup information including functional/structural
volumes and condition information from BIDS-compatible
datasets
Added ''''Import from DICOM data files''''
GUI to identify and import subjects functional/structural volumes
from DICOM files
Added ''''Import from SPM design files''''
GUI to import CONN Setup information including
functional/structural volumes and condition information from SPM
first-level design files (SPM.mat)
Added ability to run QA plots in parallel
(when using the GUI see Tools.QAplots; when using batch commands
see "help conn_batch")
Added ability to label secondary functional
datasets (from GUI and during preprocessing steps using new
''''functional_label'''' step)
Added ''''functional_smooth_masked''''
preprocessing step (spatial smoothing of functional data
aggregating across grey matter voxels only)
Added ''''functional_surface_resample'''' as
an explicit preprocessing step (converts volume-level data to
surface-level data, by resampling functional volume at the location
of FreeSurfer-generated cortical surface)
Added ''''functional_surface_smooth'''' as an
explicit preprocessing step (smooths surface-level data)
Added ''''functional_vdm_create''''
preprocessing step (creates vdm voxel-displacement map from
double-echo fieldmap acquisition files; magnitude1+phasediff or
real1+imag1+real2+imag2 or fieldmap (Hz) volumes)
(*) Added new ''''functional_vdm_create''''
step by default in ''''Indirect-Normalization pipeline'''' and
''''Surface-level pipelines'''', so these pipelines do not require
any longer that users manually create their vdm files (e.g. using
SPM FieldMap toolbox)
For back-compatibility, or if you have
already created vdm files from your fieldmap acquisition volumes,
simply remove the ''''functional_vdm_create'''' step from your
pipeline (same pipelines without these step are also saved as
*_legacy2018 in conn/utils/preprocessingpipelines)
Fixed ability to extract 1000-node network
sample timeseries (used for "QA plots" FC histogram displays) from
voxels within the MNI-space standard gray matter mask (when the
analysis mask is set to ''''explicit masking'''' and the mask is
the default MNI-space mask), or from voxels within the grey-matter
ROI (when the analysis mask is set to a different ''''explicit''''
file, ''''implicit'''' or ''''none'''')
Added rtm option to realignment preprocesing
step (choose realign-to-mean vs. realign-to-first during
preprocessing realignment step)
Gui file ''''Find'''' button in Setup tab now
uses natural sorting (non-numeric substrings sorted alphabetically,
numeric substrings sorted numerically)
Added Gui ctrl-F functionality (search
keywords) to all listbox menus
Added options to compute
alternative/additional first-level covariates, including
alternative Framewise Displacement measures (Power et al. 2012,
Jenkinson 2002) as well as options to re-compute the
''''scrubbing'''' covariate using different thresholds without
needing to re-run ART preprocessing step (see ''''compute secondary
covariates'''' option in ''''covariate tools'''' menu; see help
conn_convertl12l1covariate for scripting options)
Added GUI options to more easily update the
Denoising tab info after changes/edits in the Setup tab (e.g.
changes in condition definitions/values, first-level covariate
definitions/values, or ROI information; see ''''propagate
changes'''' in ''''condition tools'''', ''''covariate tools'''',
and ''''roi tools'''', respectively)
Updates in conn_updatefilepaths for faster
filename translations when accessing CONN projects within mounted
drives (where name of mounted drive varies depending on the machine
used to access the project)
Added percentage match value displayed in
QC-FC correlation plot (comparing robserved and expected
distributions of QC-FC correlations)
Added in group-ICA analyses the ability to
choose between different FastICA algorithms G1 (tanh; default), G2
(gauss), or G3 (pow3), as well as between different Group-ICA
back-projection algorithms GICA1, or GICA3 (default)
(*) Default group-ICA backprojection
algorithm switched from GICA1 to GICA3
For back-compatibility or mid-analysis
updates: go to first-level analysis ICA tab, select an existing ICA
analysis and change the option ''''G1 FastICA + GICA3
Back-projection'''' to ''''G1 FastICA + GICA1 Back-projection''''
if you prefer to continue using the previous GICA1 method
Added log history functionality to save and
review all screen output associated with each CONN project (also
increased the detail of information output in several preprocessing
and analysis steps to make this log more informative)
Additions to standalone release
Compiled with Matlab 2018b (MCR 9.5) and
SPM12 (7487)
Included new PC (Windows10) and Mac (macOS)
releases
19.a (internal distribution only)
19.b Cumulative patch, bug fixes and
improvements
Added new interface for recommended/standard
as well as advanced thresholding options in results explorer
voxel-based and ROI-to-ROI display
Unified results explorer interface and
options for surface-based and volume-based analyses
Added Threshold Free Cluster Enhancement
(TFCE) option to voxel-based second-level results (Smith & Nichols
2009)
Added Threshold Free Cluster Enhancement
(TFCE) option to ROI-to-ROI second-level results
Added Spatial Pairwise Clustering (SPC)
option to ROI-to-ROI second-level results (Zalesky et al.
2012)
Integrated second-level results explorer
interface for voxel-level, surface-level, and ROI-to-ROI
second-level analyses (see "help conn_display")
Added option to automatically import
fMRIPrep-preprocessed datasets (see
Tools.Convert/Import.fromFMRIPREPdataset )
Added option to define and estimate
hierarchical multi-level models (use ''''hierarchical model'''' in
Setup.Conditions to implicitly define a new condition as an
arbitrary function/transformation of other previously defined input
conditions, e.g. to estimate connectivity growth parameters of
interest in a growth-curve longitudinal analyses)
Improved ''''Plot effects'''' option in
seed-to-voxel and voxel-to-voxel results explorer windows to
provide effect-size information about individual effects and
conditions in current second-level analysis within clusters of
interest
Improved ''''Data preview'''' and ''''Plot
effects'''' options in second-level Results tab to provide
effect-size information about individual effects and conditions in
current second-level analysis at each target voxel or ROI
(*) Modified computation of Quality Control
variables ''''QC_MeanMotion'''' and ''''QC_MeanGSchange'''' to
compute average motion/GSchange measures over valid scans only
(disregarding scans already marked as outliers)
For back-compatibility or mid-analysis
updates: change the line in conn_setup_preproc.m that reads
"MEANSOVERVALIDONLY=true" to "MEANSOVERVALIDONLY=false"
Added internal check for non-estimable
contrasts when displaying second-level results design information
(part of ''''2nd-level model design information'''' button in
Results tab)
(*) Modifications to second-level analysis
multivariate "F-contrast" two-step procedure to:
1) enforce orthogonal of within-subject
contrasts (this aims to improve the replicability of
spm_est_non_sphericity F-threshold masking during ReML variance
estimation under arbitrary non-rank-reducing linear transformations
of the within-subject contrast matrix; thanks to Martyn McFarquhar
for bringing up this issue; see
https://www.nitrc.org/forum/message.php?... for
additional details)
For back-compatibility or mid-analysis
updates: in conn_process.m and conn_module_glm.m change the line
that reads "FORCEORTH=true;" to "FORCEORTH=false;"
2) base cluster-mass statistics on aggregated
F values (instead of aggregated sqrt(F) values; this aims to
provide exactly the same cluster-mass values for clusters resulting
from two-sided GLM univariate contrasts as those resulting from GLM
multivariate contrasts when both analyses effectively test the same
null hypothesis)
For back-compatibility or mid-analysis
updates: in conn_displayroi.m conn_randomise.m and conn_vproject.m
change the line that reads "DOSCALEF=true;" to
"DOSCALEF=false;"
3) changed default Wilks'''' Lambda
statistics procedure from Bartlett''''s Chi-square approximation to
Rao''''s F approximation (this aims to provide increased accuracy
for small sample sizes)
For back-compatibility or mid-analysis
updates: in conn_glm.m change the line that reads
"BBDEFAULT=''''BB_RAO'''';" to
"BBDEFAULT=''''BB_BARTLETT'''';"
(*) Modification to optional CONN outputs
generated when selecting the option ''''create confound-corrected
timeseries'''' to: 1) output one separate NIFTI file per
run/session (prepending ''''d'''' letter to original functional
filenames); and 2) add back the average BOLD timeseries (one value
per voxel) in the resulting denoised volumes (this is intended to
maintain anatomical-feature information in the denoised data; e.g.
used by SPM implicit masking procedure)
For back-compatibility or mid-analysis
updates: in conn_process.m change the line that reads
"DONEWOUTPUTCONFCORR=1;" to "DONEWOUTPUTCONFCORR=0;"
Added
''''structural_normalize_preservemasks'''' and
''''functional_normalize_indirect_preservemasks'''' preprocessing
steps to keep externally-generated tissue-class maps (e.g.
FreeSurfer-generated Grey/White/CSF masks) aligned to structural
data during structural or indirect-functional normalization
steps
Added ''''interleaved (Philips)''''
slice-order option in Slice Timing Correction preprocessing step
procedure (thanks to Pravesh Parekh for bringing up this issue and
providing the documentation; slice order in Philips "interleaved"
sequences defined as
cell2mat(arrayfun(@(n)n:K:N,1:K,''''uni'''',0)), where N is the
number of slices and K is the interleave number =
round(sqrt(N))
Added ''''functional_regression''''
preprocessing step to perform temporal regression and removal of
temporal components-of-no-interest to functional volumes
Added ''''functional_bandpass''''
preprocessing step to perform temporal band-pass filtering to
functional volumes
Added ''''functional_vdm_apply''''
preprocessing steps to perform Susceptibility Distortion Correction
from VDM maps to functional volumes (independently of realignment,
unlike the existing functional_realign&unwarp&fieldmap
preprocessing step)
Added conn_module(''''glm'''',...) options
for user-defined ROI-to-ROI second-level analyses (see "doc
conn_module" and "doc conn_mtx_write")
19.c (cumulative patch for 19.b)
patch to display group-labels when using ROIs
from atlas.nii file (''''CONN atlas apriori ROI order/clusters''''
in ROI-to-ROI second-level results) and networks.nii file (''''CONN
networks apriori ROI order/clusters'''' option in ROI-to-ROI
second-level results)
patch to fix error when using
conn_module(''''glm''''...,''''mask'''',...) to run ROI-to-ROI
second-level analyses with masking
(*) patch to fix ''''mask with grey
matter'''' option in Setup.ROIs tab to mask within thresholded grey
matter mask instead of original grey matter mask (see conn_batch
binary_threshold and binary_threshold_type for additional options;
change erosion settings "binarization threshold" field to 0 for
back-compatibility)
patch to add ''''export data'''' option in
ROI-to-ROI second-level results (exports ROI-to-ROI connectivity
matrices in matrix NIFTI format, which can then be entered as input
to conn_module(''''glm'''',...))
patch to add ''''graphic options'''' button
in ROI-to-ROI seccond-level results GUI (shows/hides advanced
graphic-options menubar) (thanks to Joey Contreras for bringing up
this issue;
https://www.nitrc.org/forum/forum.php?th...)
patch to add Yeo2011 7-networks template (in
conn/utils/otherrois) as ROI or as template for ICA component
identification (spatial match to template) (thanks to Yiquan for
suggesting this addition
https://www.nitrc.org/forum/message.php?...)
patch to add ''''merge (not-in-union)''''
option to "conditions tool" menu allowing to compute an exclusive
conjunction of several conditions (those scans/timepoints not
already covered by one or several other conditions; e.g. to
explicitly define a reference/baseline effect from an event related
design) (thanks to Alex for suggesting this addition
https://www.nitrc.org/forum/forum.php?th...)
20.a (internal distribution only)
20.b Cumulative patch, bug fixes and
improvements
patch to fix color scaling in R2R display
(thanks to Paul Summers for bringing this issue up)
patch to distributed processing to fix memory
problems when merging large number of HPC jobs (thanks to Victoria
Okuneye for bringing this issue up)
Added new interface for defining first-level
analyses, including list with most common connectivity
analyses/measures and their default options
Added new interface for defining second-level
anayses, including QDEC-style "layman''''s terms" interactive
descriptions of second-level model, as well as list of suggested
analyses automatically-populated based on each CONN project
2nd-level covariates (see ''''Results (2nd-level)'''' tab)
Added brain & connectivity-matrix displays of
computed single-subject connectivity measures in first-level
analysis GUI
Changed normalization setting "interp"
default value to Trilinear interpolation during interpolation of
anatomical images (kept the same default Bspline interpolation
method for interpolation of functional images) (this change is
meant to avoid small negative values in resampled anatomical
images, which may cause issues when exporting these images to other
software packages)
Modified slice-display default background
reference image to ICBM (nlin_asym_09c) normalized using SPM12/CONN
default options (in prior versions this background reference image
was the same ICBM template but without SPM12 normalization
correction)
Modified 3d-display cortex and white surfaces
to freesurfer tesellation of ICBM (nlin_asym_09c) normalized using
SPM12/CONN default options (in prior versions these surfaces were
the fsaverage6 pial&white surfaces)
Added connectivity-matrix display to
ROI-to-ROI results explorer window (see "matrix display" and
"matrix print" options in the GUI)
Added option to manually define&edit ROI
order and clusters in ROI-to-ROI results explorer window (see
''''manually define ROI order/clusters'''' GUI option, or
''''roi.order'''' options in doc conn_display)
Added option to display&edit 2nd-level
covariate values in table format (to make it simpler to change the
values of one individual subject; see Setup Covariates (2nd-level)
tab)
Added option to automatically create
interaction terms among 2nd-level covariates, and option to
discretize/dummy-code categorical covariates (see ''''covariate
tools'''' in Setup Covariates (2nd-level) tab)
Modified voxel-level results-explorer TFCE
display to report only number of local maxima (prev. version
reported number of both local maxima&minima)
Added backup copy of conn_*.mat project file
stored as conn_*/bakfile.mat (backup contains copy of last
successfully-loaded version of the conn project file)
Added more flexible options to
Tools.Run.SecondLevelResults menu (single-click run multiple
second-level analyses, including different models and different
sources/measures)
Added group-MVPA ''''summary'''' display
showing cumulative percent variance in multivoxel patterns
explained by group-MVPA components (see second-level results
tab)
Added ''''functional_load_from''''
preprocessing steps to load functional files from a
previously-saved secondary dataset (e.g. saved using
functional_label_as*, then loaded using functional_load_as*)
Updated fmriprep compatibility to fmriprep
20.2.0
Added fmriprep options to import data to
derivatives/conn folder and read event information from raw-data
folders tsv files
Added option to ROI-to-ROI results explorer
GUI to display/import connectivity values from user-defined masks
(e.g. those created using ''''export mask'''' from other
second-level analyses)
20.c (internal distribution only)
21.a Cumulative patch, bug fixes and
improvements
Fixed bug when displaying multivariate RRC
second-level analyses computed using external data /
conn_module(''''glm'''',...) commands
patch to keep DICOM manifest across CONN
project saves
patch to read TOPUP fieldmap files
(*) added support in ''''functional creation
of Voxel-Displacement Maps'''' preprocessing step for importing
BLIP polarity from PhaseEncodingDirection field for non-axial
acquisitions (i/j/k signs are now interpreted as BLIP=sign([0 1 0
0]*vol.mat*[i j k 0]'''')
For back-compatibility or mid-analysis
updates: if your analyses were running the preprocessing step
''''functional Creation of voxel-displacement map (VDM) for
Susceptibility Distortion Correction'''' and the field ''''BLIP
direction'''' was left empty (so that information was read from
.json files) and you prefer to continue using the old/previous
convention, then set the BLIP direction manually by entering in the
''''BLIP direction'''' field the value -1 if the .json files
PhaseEncodingDirection field is ''''j+'''' and the value +1 if the
.json files PhaseEncodingDirection field is ''''j-'''' (note: this
assumed top-to-bottom sorting)
Added submit_delay option to
parallelization/HPC job submission (this can be used to reduce the
load on the cluster job scheduler when handling multiple job
requests)
Added option to create .mtx.nii file output
with estimated time-varying RRC matrix when running dynamic
ICA
Added -v7.3 version save as backup option if
default project save fails
Updated BIDS compatibility to v1.6.0
Added script for cat12-to-Freesurfer
conversion
Added filter option to
''''function_regression'''' preprocessing step (to allow
filtered-regressor option when using
conn_module(''''preprocessing'''',...) to run aCompCor
denoising)
Added ''''view details'''' checkbox in
2nd-level GUIs to simplify threshold-setting options
Added option to break single-variable .mat
files into multiple-timeseries covariates
Added option for using scrubbing based on
thresholding external timeseries (including single-measure
timeseries)
Added option to create single-voxel-ROIs from
mask (see Setup.ROIs tab)
Added ''''import values'''' functionality to
conn_display when run outside of any CONN project
Added QC_DOF_Session# quality control
2nd-level covariate computing effective degrees of freedom for each
subject/session after denoising
Added conn_tcpip for TCP/IP based
communications and conn_server for client/server communication
between two CONN sessions
Added "conn_remotely" for working with CONN
projects stored remotely using SSH protocol for communications (see
"help conn_remotely" for details)
Added Inter-hemispheric Correlation (IHC)
1st-level analyses (voxel-level correlation between a voxel and its
contralateral voxel; note: for 3D volume functionals contralateral
voxel is based on voxel coordinates (x,y,z) matched to (-x,y,z);
for 2D surface functionals contralateral vertex is based on a
non-linear match in spherical coordinates between Freesurfer left-
and right- hemisphere surface-curvature templates - vertex i in
left-hemisphere surface matched to vertex LEFT2RIGHT(i) in
right-hemisphere surface, vertex j in right-hemisphere surface
matched to vetex RIGHT2LEFT(j) in left-hemisphere surface; see
conn/utils/surf/lhrh.mat)
Added "view-only" mode for avoiding conflicts
when viewing a project while another user may be actively working
with the same project
22.a Cumulative patch, bug fixes and
improvements
Added support for Secure Shell on remote
connections from clients running PC/Windows
Added ''''Real ROI shape'''' option to
second-level ROI displays (see "help conn_mesh_display")
Added Maximum-Intensity-Projection coloring
to results explorer ''''Glass display'''' view
Added colorbar to 2nd-level results explorer
printouts
Added ''''defaultMNI_withlesion''''
preprocessing pipeline to incorporate lesion masks in CONN
preprocessing steps
Added
''''structural_segmentation&normalization_withlesion''''
preprocessing step: uses a subject-space lesion mask as part of
structural normalization, normalizes subject-space lesion ROI (e.g.
to be used as seeds or masks), and creates a new subject-specific
TPM dataset incorporating a lesion tissue class (e.g. to be used by
functional normalization during a direct normalization
pipeline)
Added
''''functional_segment&normalize_indirect_withlesion''''
preprocessing step: uses a subject-space lesion mask as part of an
indirect normalization pipeline (outputs as above)
Added ''''functional_mask'''' preprocessing
step: implicit or explicit masking of functional data
Added ''''structural_mask'''' preprocessing
step: implicit or explicit masking of structural volume
Extended ''''functional_smooth_masked''''
preprocessing step to use any custom mask (same as
''''functional_mask'''' step; see mask_names_func and
mask_inclusive_func fields)
Added ''''functional_roiextract''''
preprocessing step: import ROI BOLD timeseries as 1st-level
covariates
Added ''''Preprocessing.rmask'''' batch
option to ''''functional_realign'''' preprocessing step in order to
allow enabling/disabling field-of-view masking of resampled
realigned data
Added ability to model acquisition/scan time
for sparse-acquisition task-activation analyses in EL/FL
modules
Simplified Setup.functional gui by moving
secondary-datasets into a new "Setup.other" tab
Added new conn_table_display for contingency
data and ROI-to-ROI connectivity displays
Added .tsv outputs to mask creation in
results explorer window, saving anatomical information about the
resulting suprathreshold clusters in structured format
Changed curvature background displayed on 3D
surfaces to reflect ICBM MNI 2009b
Added option for asymmetric windows around
outliers in the ''''scrubbing''''
conn_convertl12l1covariate.m
Added BlueWhiteRed colormap option for 3D
displays
Added affine regularization option
Setup.preprocessing.affreg to all segmentation&normalization
preprocessing steps
Added QC_PVS (percent of valid scans),
QC_NORM_func (percent match of white matter functional
normalization mask to template), QC_NORM_struct (percent match of
white matter structural normalization mask to template) quality
control measures
Fix issue when connecting to a remote server
that does not support SCP (switches to using SSH for transfering
text files)
Added option to specify
Setup.preprocessing.warpreg parameters for normalization
preprocessing steps
Added ''''export raw data'''' option to ROI
display in results explorer GUI
Added Setup.preprocessing.tpm_overwrite
option to preprocessing lesion normalization procedure, in order to
allow several sequential iterations improving the TPM+mask
templates
Added ClosenessCentrality (inverse average
path length), EigenvectorCentrality (eigenvector of largest
eigenvalue of adjacency matrix), and Eccentricity (maximum path
length) measures to graph analyses.
Added conjunction_threshold option to rex for
ROI conjunctions with localizer maps
Added ''''network display'''' button to
voxel-level results explorer window, showing for each significant
cluster the connectivity between that cluster and the rest of the
brain (and additional options)
Added ''''Write Methods'''' functionality
(see Tools.WriteMethod and conn_reference.m) creating automated
text, distributed under a public domain dedication license,
describing all the specific preprocessing, denoising, 1st- and 2nd-
level analyses steps used in your individual CONN project.
Added new ''''group-MVPA.Summary'''' tab
displaying entire voxel-to-voxel connectome (like AFNI''''s
InstaCorr but combining the data across all subjects in your
dataset), as well as visual descriptions of each individual fc-MVPA
eigenpattern characterizing the observed variability in
connectivity maps across subjects and conditions.
Updated manual
note: the symbol (*) in any of the lists
above indicates changes that users need to pay special attention to
when upgrading mid-analysis, as they may produce different results
compared to previous versions (users may want to hold update until
analyses are finished or take special precautions to ensure
continuity; instructions for exact replicability with
previous-version analyses are described in each case)
changes in progress or projected:
add simpler options to use alternative
reference brain surfaces in 3d displays (e.g. for pediatric or
non-human analyses)
add integration with CAT12
add interoperability with BCT measures
add interoperability with Matlab NN/ML
toolbox
add voxel-level regressors to second-level
analysis options
add import graph-theory measures as
second-level covariates
add batch.mat second-level analysis file to
second-level results folder
add support for flexible ROIs
add possibility to share/download neuromarker
definitions
add integration with NITRC-IR image
repository
add integration with NITRC-EC
environments
