Notes:

Release Name: conn v.25.b

Notes:

CONN main release (25.b)


Installation instructions: https://conn-toolbox.org/installation&nb...


 

Changes:



  • 25.b Cumulative patch, bug fixes and improvements





  • Update conn_slice_display command-line help





  • Bug fix in conn_slice_display (it was displaying the freesurfer pial/white contours in the incorrect location if the reference brain.mgz image was not in standard recon-all orientation)





  • Added command-line options and edit documentation of conn_polar_display function





  • Merge pull request #10 from LeonHWan/master [feat] option to wite-out regions below activation threshold in the ...





  • Added "HPC settings" option to select whether each computational node should use multithreading or a single computational thread (conn_jobmanager settings)





  • Removed background box in "import files" gui menus





  • Added multiple-sites option to batch example file conn_batchexample_qcplot.m





  • Force message box gui to foreground when preprocessing to more easily identify when preprocessing is still running





  • Added covariate control option to QC-FC correlations in 'QA plots'





  • Fixed bug in qaplots when running plots in parallel without first saving conn project





  • Changed label from 'somatosensory' to'sensorimotor' in utils/otherrois/Yeo2011.nii networks file





  • Bug fix in slice-intensity-correction method (error when using after a functional_removescans step)





  • Added support for SPM25 SCOPE computation of vdm files from opposite phase encoding direction files





  • Added more flexible masked-smoothing options to the 'functional_smooth_masked' preprocessing step (include mask, exclude mask, and preserve boundaries)





  • Bug fix (include _fmap.nii files) when importing from BIDS





  • Bug fix (fixes issues interpreting/displaying SPM25 version number)





  • Bug fix (importing several FMAP files for each subject when selecting and importing multiple subjects and sessions in the GUI)





  • Minor GUI enhancements (display Spatial/Temporal/Summary buttons on top for ICA, PCA, & MVPA results tabs)





  • Add an option to also remove first few initial scans when using the 'create scrubbing covariate' menu in the GUI





  • Added an option to enter FMAP files in opposite order to SCOPE





  • Bug fix incorrect output folder when using SCOPE





  • Bug fix (parallelization of v2v measures from GUI was fixed to using N=1 jobs)





  • Added error message when attempting to extract data from a surface-level .surf.nii functional file using a volume-level ROI file (or a warning if there is an alternative .vol.nii functional file available)





  • Fixes for SPM25 compatibility





  • Added ability to make changes to current project while remote jobs are running





  • Added ability to run a new set of background/remote jobs before a previous set has finished





  • Added ability to add control covariates in QC-FC plots





  • Added aggregate (instead of per-run) quality control plots after denoising





  • Added QC_DOF, QC_MeanFC and QC_StdFC measures for quality control (degrees of freedom after denoising, mean and standard deviation of FC distribution after denoising) computed each time the "FC distribution" plot is run





  • QC_OutlierSubjects and related measures (computed each time the "QC histogram" plot is run) now take into account the "directionality" of most QC measures (low values are "bad" for QC_ValidScans|QC_ProportionValidScans|QC_NORM_func|QC_NORM_struct|QC_DOF, and high values are "bad" for QC_InvalidScans|QC_MeanMotion|QC_MaxMotion|QC_StdFC). For the rest of measures both directions are used when identifying potential outlier subjects





  • Added option to remove "session-invariant" confounds during denoising (confounds modeled as linear factors on the BOLD signal with regressor coefficients that do not vary across runs/sessions for each given subject)





  • Bug fix (.json file not found when associated functional file is a surface nifti file)





  • Fix issue when importing fMRIPrep confounds having a NaN value in first timepoint (fix by converting those NaN's to 0's)





  • Added Setup.rois.regresscovariateschoose batch field (and associated GUI elements) to allow users to manually select 1st-level covariates that will be regressed out before Principal Component Analyses when computing aCompCor WM and CSF timeseries





  • Added ability to specify control variables when running QC-FC quality assurance plots





  • Added manual temporal-weighting option when defining conditions (manually specify a first-level covariate containing an individual condition's temporal weights). This can be used, for example, when importing SPM first-level designs to define conditions exactly in the same way that they appear in SPM's first-level design matrix.





  • Added conn_createsubsetrois function to select or combine individual ROIs from an atlas file





  • Added internal conn_displayroi DOSORT variable to allow users to select the order of ROIs when exporting data from a second-level RRC analysis





  • Added conn_fileutils('filecopy',...) now works with remote files as well





  • Added QC_SPM_taskeffects covariate when using the "import from SPM" functionality in CONN containing task effects in SPM design





  • Fix to conn_merge to update secondary dataset names merging multiple projects while disregarding the current project (disregardcurrent option)





  • Added check&fix when running conn_module('GLM',...) for masked ROI-to-ROI second-level analyses to warn users if the order of the ROIs in the mask differs from the the order of the ROIs in the data





  • Added conn_qcoptimize function (under development; users may use this function to help optimize choice of denoising parameters and list of valid subjects to maximize the QC-FC percentage match level criterion)





  • Bugfix in conn_vproject GUI when switching from p-value to F-value thresholds (now the displayed F-value is chosen to produce the same cutoff than the previously selected p-value and viceversa)





  • Added fl2conn option to FL (creates CONN project from selected subjects in FL experiment)





  • Added conn_clusterregress implementing clustered regression models for massively multivariate predictive analyses





  • Added new conn_menu_plotscatter and conn_mtx_braindisplay functions for scatterplot and .mtx.nii data displays





  • Added conn_nii2gz function for .nii.gz file creation





  • Added conn_h52rr function to transform denoised timeseries .h5 data files to .mtx.nii connectivity-matrix format





  • Fix GUI issues when using the latest Matlab 2025a release





  • Added module CPM for connectome predictive models





  • Continue fixes for new R2025a graphic rendering functions





  • Continue fixes for new R2025a & R2025b graphic rendering functions





  • Continue fixes for new R2025a & R2025b graphic rendering functions (use new light/dark theme options in Matlab)





  • Added 'slice-viewer' and 'display coregistration with user-defined overlay' options to functional-tools menu





  • Added QC_WelchSatterthwaite quality control measure (when planning to use DOF for first-level stats this provides a more accurate estimation of effective degrees of freedom using a WS approximation)








  • Added "Quality Control" section to "Methods" boilerplate text autogenerated by CONN from the project's denoising&QA options





  • Added Schaefer-400 atlas to list of default ROIs for new projects (labels extended to include MNI coordinates and Harvard-Oxford anatomical description)





  • Added conn_meshroi_display for 3D display of ROI areas





  • Added option in conn_displayroi to resort atlases differently in "circle" display (see coords2 in conn_roiclusters) and in "matrix" display (see coords1 in conn_roiclusters)





  • Added option to reduce visual clutter in matrix display view by reducing the numbers of labels displayed





  • (*) Added to default preprocessing pipeline the option to create a new dataset in subject-space (coregistered to structural, prior to inter-subject normalization) in order to facilitate the use of subject-space ROIs. To skip this change and continue using the previous pipeline use Preprocessing->Load and select the pipeline at utils/preprocessingpipelines/defaultMNI_legacy2023.mat





  • Modify the ROI orders/groups for CONN's Harvard-Oxford atlas based on analysis of a larger dataset (see conn/rois/atlas.groups.info for details) and adapt labels to better match current network-level naming conventions (note: for replicability if you prefer to use the previous order/groups, in the results explorer window select the option to load order/groups from a file and select the file conn/utils/otherrois/v1_atlas.groups.mat)





  • Added option (in Denoising tab) to select a user-defined group of subjects for Data Sensitivity score computations





  • Added option (in Results tab) to add ExcludeOutlierSubjects as a control variable in your second-level analyses (if you wish to enforce the participant-selection suggestion provided in the Denoising and Quality Control tab)





  • Several bugfixes to allow simultaneous submission of multiple groups of jobs to cluster environments





  • Bugfix in creation of ExcludeOutlierSubjects covariate from GUI when using alternative exclusion criteria





  • Added Schaefer references to Methods boilerplate text





  • Added options (in Setup.Options) to export denoised ROI BOLD timecourses as .csv files, and to export RRC connectivity matrices as .mtx.nii files





  • Added display of ROI clusters information in conn_mtx_display





  • Added 'Denoising & QC tools' options in Denoising tab to: a) reset all denoising options to initial default values; b) reset all denoising options to empty values (for skipping denoising); and c) re-computing one or all Data Validity/Quality/Sensitivity scores





  • When making changes in the Setup.ROIs/Conditions/Covariates tabs for a project that has already been processed and clicking on 'Apply&Update' CONN will now ask whether you want to update only the changes in this section or across other Setup sections as well





  • Minor GUI-design changes in Setup/Denoising tabs to improve clarity