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Notes:
CONN main release (22a) Installation instructions: https://web.conn-toolbox.org/resources/i...
Changes:
Changes in release 22.a Cumulative patch, bug fixes and
improvements 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. 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 '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
ClosenessCentrality (inverse average path length),
EigenvectorCentrality (eigenvector of largest eigenvalue of
adjacency matrix), and Eccentricity (maximum path length) measures
to graph analyses. Added support for Secure Shell on remote
connections from clients running PC/Windows 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 '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 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
conjunction_threshold option to rex for ROI conjunctions with
localizer maps Updated manual Changes in previous releases
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 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) Added links to video tutorials and additional resources
hosted on http://www.conn-toolbox.org 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)
Fixed/Improved randomization non-parametric procedure to include
group-vs-single-subject comparisons (thanks to Stephen Larroque;
see https://www.nitrc.org/forum/forum.php?th... for
additional details) (*) 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 fix
logged description of denosing procedure parameters (thanks to
James Ford for bringing this issue up; https://www.nitrc.org/forum/forum.php?th...)
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 error
when using analysis masks close to image borders (thanks for Jan
Maloman for bringing up this issue; https://www.nitrc.org/forum/forum.php?th...)
patch to fix error when importing BIDS datasets without zero-padded
subject ID numbers (thanks to Hongru Zhu for bringing up this
issue; https://www.nitrc.org/forum/forum.php?th...) (*)
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 ability to read subject-specific freesurfer annotation
.annot files (thanks to Amy Bouchard 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 conn_vol_read/write functions to complement
conn_mtx_* and conn_surf_* functions (see http://www.conn-toolbox.org/resources/do... for details)
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_module EL" for using a combination of SPM and
CONN functionality for task activation analyses of fMRI data (see
http://www.conn-toolbox.org/resources/ev... for details)
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
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