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) 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) 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, '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/clusters (atlas.nii ROIs only) [option=3] Use CONN networks apriori order/clusters (networks.nii ROIs only) [option=4] Import ROI order/clusters from input file filename [option=5] Import ROI order/clusters from clipboard [option=6] Export ROI order/clusters to output file filename [option=7] Export ROI order/clusters to clipboard 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