CONN display help

  conn_display 

         displays second-level analysis results

BASIC SYNTAX:

   hf = conn_display(SPMfilename)    SPMfilename : input file name (typically SPM.mat) containing second-level analysis results                  either from voxel-based analyses, surface-based analyses, or ROI-to-ROI analyses    hf          : output handle to results figure   e.g. conn_display('/results/SPM.mat'); 

ADVANCED OPTIONS FOR VOXEL- AND SURFACE- LEVEL RESULTS FIGURES (applied when creating a new results figure)

   hf = conn_display(SPMfilename, ncon, style)    SPMfilename : input file name (typically SPM.mat) containing second-level analysis results    ncon        : input contrast number (if multiple contrasts are defined in 2nd-level results SPM.mat file)    style       : inpput voxel/cluster threshold settings (see Nieto-Castanon, 2020 for details about these methods; www.conn-toolbox.org/fmri-methods)                    [style=1] for default settings #1 : parametric statistics (Gaussian Random Field theory, Worsley et al. 1996) (default for volume-based results)                     [style=2] for default settings #2 : nonparametric statistics (permutation/randomization analyses, Bullmore et al. 1999) (default for surface-based results)                    [style=3] for default settings #3 : nonparametric statistics (Threshold Free Cluster Enhancement, Smith and Nichols, 2007)    hf          : output results explorer window handle (which can be used in advanced options described below)   e.g. conn_display('/results/SPM.mat',1,3); 

ADVANCED OPTIONS FOR VOXEL- AND SURFACE- LEVEL RESULTS FIGURES (applied to an existing results figure)

    conn_display(hf, 'surface_print', filename)       prints image with current results projected to the cortical-surface  conn_display(hf, 'surface_view', filename)        displays image with current results projected to the cortical-surface  conn_display(hf, 'volume_print', filename)        prints image with current results on 3d brain  conn_display(hf, 'volume_view', filename)         displays image with current results on 3d brain  conn_display(hf, 'slice_print', filename)         prints image with current results on individual slices  conn_display(hf, 'slice_view', filename)          displays image with current results on individual slices  conn_display(hf, 'glass_print', filename)         prints image with current results on 3d glass-brain  conn_display(hf, 'glass_view', filename)          displays image with current results on 3d glass-brain  conn_display(hf, 'export_mask', filename)         exports NIFTI mask file with current results  conn_display(hf, 'close')                         closes results explorer window  conn_display(hf, 'fwec.option', style)            modifies default threshold settings (see 'style' valid values above)  conn_display(hf, 'fwec.voxellevel.value', value)  modifies voxel-level threshold value  conn_display(hf, 'fwec.voxellevel.type', type)    modifies voxel-level threshold type                                                    [type=1] p-uncorrected                                                    [type=2] p-FDR corrected                                                    [type=3] p-FDR corrected (TFCE)                                                    [type=4] p-FWE corrected (TFCE)                                                    [type=5] F/T/X stat  conn_display(hf, 'fwec.voxellevel.side', type)    modifies voxel-level threshold directionality                                                    [side=1] one-sided (positive)                                                    [side=2] one-sided (negative)                                                    [side=3] two-sided  conn_display(hf, 'fwec.clusterlevel.value', value) modifies cluster-level threshold value  conn_display(hf, 'fwec.clusterlevel.type', type)    modifies cluster-level threshold type                                                     [type=1] cluster-size                                                    [type=2] cluster-size p-FWE corrected                                                    [type=3] cluster-size p-FDR corrected                                                    [type=4] cluster-size p-uncorrected                                                    [type=5] peak-voxel p-FWE corrected                                                    [type=6] peak-voxel p-uncorrected                                                    [type=7] cluster-mass                                                    [type=8] cluster-mass p-FWE corrected                                                    [type=9] cluster-mass p-FDR corrected                                                    [type=10] cluster-mass p-uncorrected  conn_display(hf, 'fwec.clusterlevel.parametric', type) modifies cluster-level parametric statistics option                                                    [type=1] parametric statistics (Random Field Theory)                                                    [type=2] non-parametric statistics (Randomization/Permutation tests) 

ADVANCED OPTIONS FOR ROI-to-ROI RESULTS FIGURES (applied when creating a new results figure)

   hf = conn_display(SPMfilename, ncon, style)    SPMfilename : input file name (either SPM.mat or ROI.mat file) containing second-level analysis results    ncon        : contrast number (if multiple contrasts are defined in 2nd-level results SPM.mat file)    style       : voxel/cluster threshold settings (see Nieto-Castanon, 2020 for details about these methods; www.conn-toolbox.org/fmri-methods)                    [style=1] for default settings #1 : parametric multivariate statistics (Functional Network Connectivity, Jafri et al., 2008)                    [style=2] for default settings #2 : non-parametric statistics (Spatial Pairwise Clustering, Zalesky et al., 2012)                    [style=3] for default settings #3 : non-parametric statistics (Threshold Free Cluster Enhancement, Smith and Nichols, 2007)                    [style=4] for alternative settings for connection-based inferences : parametric univariate statistics (connection-level inferences, FDR corrected, Benjamini & Hochberg, 1995)                    [style=5] for alternative settings for ROI-level inferences: parametric multivariate statistics (ROI-level inferences, FDR corrected, Benjamini & Hochberg, 1995)                    [style=6] for alternative settings for network-level inferences: non-parametric statistics (network-level inferences, Network Based Statistics, Zalesky et al., 2010)    hf          : output results explorer window handle (which can be used in advanced options described below)   e.g. conn_display('/results/SPM.mat',1,3); 

ADVANCED OPTIONS FOR ROI-to-ROI RESULTS FIGURES (applied to an existing results figure)

   conn_display(hf, 'print', filename)                       prints image with current results  conn_display(hf, 'glass_print', filename)          prints image with current results on 3d glass-brain  conn_display(hf, 'glass_view', filename)           displays image with current results on 3d glass-brain  conn_display(hf, 'matrix_print', filename)        prints image with current results on ROI-to-ROI matrix view  conn_display(hf, 'matrix_view', filename)         displays image with current results on ROI-to-ROI matrix view  conn_display(hf, 'export_mask', filename)         exports NIFTI mask file with current results  conn_display(hf, 'menubar')                       displays/hides menubar with advanced display options  conn_display(hf, 'close')                         closes results explorer window  conn_display(hf, 'roi.select' [,ROInames])        modifies selection of ROIs  conn_display(hf, 'roi.order',option [,filename])  modifies ROI sorting procedure                                                    [option=1] Use hierarchical clustering method (default)                                                    [option=2] Use CONN atlas apriori order/groups (atlas.nii ROIs only)                                                    [option=3] Use CONN networks apriori order/groups (networks.nii ROIs only)                                                    [option=4] Load ROI order/groups from input file filename (see 'doc conn_roiclusters' for details)                                                    [option=5] Load ROI order/groups from clipboard                                                    [option=6] Save ROI order/groups to output file filename                                                    [option=7] Save ROI order/groups to clipboard                                                    [option=8] Manually define ROI order/groups  conn_display(hf, 'fwec.option', style)            modifies default threshold settings (see 'style' valid values above)  conn_display(hf, 'fwec.connectionlevel.value', value) modifies voxel-level threshold value   conn_display(hf, 'fwec.connectionlevel.type', type) modifies voxel-level threshold type                                                    [type=1] p-uncorrected                                                    [type=2] p-FDR corrected                                                    [type=3] p-FDR corrected (TFCE)                                                    [type=4] p-FWE corrected (TFCE)                                                    [type=5] F/T/X stat  conn_display(hf, 'fwec.connectionlevel.side', type) modifies voxel-level threshold directionality                                                    [side=1] one-sided (positive)                                                    [side=2] one-sided (negative)                                                    [side=3] two-sided  conn_display(hf, 'fwec.clusterlevel.value', value) modifies cluster-level threshold value  conn_display(hf, 'fwec.clusterlevel.type', type)    modifies cluster-level threshold type                                                     [type=1] network-level p-uncorrected (NBS mass/intensity)                                                    [type=2] network-level p-FDR corrected (NBS mass/intensity)                                                    [type=3] network-level p-FWE corrected (NBS mass/intensity)                                                    [type=4] cluster-level p-uncorrected (MVPA omnibus test)                                                    [type=5] cluster-level p-FDR corrected (MVPA omnibus test)                                                    [type=6] cluster-level p-uncorrected (SPC mass/intensity)                                                    [type=7] cluster-level p-FDR corrected (SPC mass/intensity)                                                    [type=8] cluster-level p-FWE corrected (SPC mass/intensity)                                                    [type=9] ROI-level p-uncorrected (MVPA omnibus test)                                                    [type=10] ROI-level p-FDR corrected (MVPA omnibus test)                                                    [type=11] ROI-level p-uncorrected (ROI mass/intensity)                                                    [type=12] ROI-level p-FDR corrected (ROI mass/intensity)                                                    [type=13] ROI-level p-FWE corrected (ROI mass/intensity)                                                    [type=14] none    see also CONN_MODULE