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Notes:
Changes:
CONN 17.f release change log
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 reference figures displaying the default atlas and network
ROI labels (
Added links to video tutorials and additional resources hosted on http://www.conn-toolbox.org
Cumulative CONN17 release change log:
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
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