Release Name: conn v.18.b

CONN 18b main release

Installation instructions:

CONN 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