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Updated: Added MPathI tutorial, added prep_for_connectivity or RL modeling tutorial
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‎example_help_files/canlab_help_annotate_thresholded_results_map.m

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%% Load a test map to use as an example
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ns = load(which('neurosynth_data_obj.mat'));
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test_map = get_wh_image(ns.topic_obj_reverseinference, 1); % somatosensory topic
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%% Run annotations
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annotate_binary_results_map(test_map)
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<div class="content">
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<h2>Contents</h2>
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<div>
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<ul>
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<li>
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<a href="#1">Load a test map to use as an example</a>
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</li>
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<li>
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<a href="#2">Run annotations</a>
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</li>
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</ul>
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</div>
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<h2 id="1">Load a test map to use as an example</h2>
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<pre class="codeinput">ns=load(which(<span class="string">'neurosynth_data_obj.mat'</span>));test_map=get_wh_image(ns.topic_obj_reverseinference,1);<span class="comment">% somatosensory topic</span>
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</pre>
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<h2 id="2">Run annotations</h2>
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<pre class="codeinput">annotate_binary_results_map(test_map)
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</pre>
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<pre class="codeoutput">Transmodal vs. unimodal: Principal gradient of functional connectivity
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</pre>
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<img vspace="5" hspace="5" src="canlab_help_annotate_thresholded_results_map_01.png" alt=""> <img vspace="5" hspace="5" src="canlab_help_annotate_thresholded_results_map_02.png" alt=""> <pre class="codeoutput">Allen brain project transcriptomic gradients
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</pre>
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<img vspace="5" hspace="5" src="canlab_help_annotate_thresholded_results_map_03.png" alt=""> <pre class="codeoutput">Neuromaps PET neurochemical tracer maps
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</pre>
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<img vspace="5" hspace="5" src="canlab_help_annotate_thresholded_results_map_04.png" alt=""> <pre class="codeoutput">
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Name Pearson's r
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5HT1a 0.0229
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5HT1a 0.0319
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5HT1b 0.0451
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5HT1b 0.0831
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5HT1b 0.0451
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5HT2a 0.0330
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5HT2a 0.0326
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5HT2a 0.0245
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5HT4 0.0056
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5HT6 0.0566
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5HTT -0.0327
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5HTT -0.0054
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a4b2 -0.0081
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CB1 0.1152
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CB1 0.0581
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D1 -0.0247
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D2 -0.0069
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D2 -0.0012
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D2 -0.0077
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D2 0.0165
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DAT -0.0038
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DAT -0.0621
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GABAa 0.0610
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GABAabz 0.0736
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H3 0.0245
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M1 0.0879
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mGluR5 0.0777
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mGluR5 0.0906
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mGluR5 0.1215
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MOR -0.0416
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MOR 0.0048
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NET 0.0835
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NET 0.1811
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VAChT 0.0143
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VAChT -0.0073
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VAChT 0.0200
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Neurosynth topic and term maps
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Neurosynth topics - forward inference maps
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Test image 1
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..cs\v4-topics-100_0_stimulation_somatosensory_tms_pFgA_z_FDR_0.01.nii
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_____________________________________________________________________
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r_lowest Term_or_Topic_lowest r_highest Term_or_Topic_highest
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_________ _____________________________ _________ _____________________________
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-0.072766 {'Word Processing' } 0.60286 {'Sensory Stimulation' }
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-0.063182 {'Emotion face' } 0.2544 {'Pain Perception' }
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-0.062233 {'Familiarity &amp; recognition'} 0.2481 {'Motor movements' }
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-0.059672 {'Depression &amp; Disorders' } 0.24004 {'Motor control' }
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-0.058889 {'Language comprehension' } 0.07949 {'Motor Coordination' }
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-0.057834 {'Reading &amp; Writing' } 0.07842 {'Creativity &amp; Acupuncture '}
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-0.056539 {'Cognitive Conflict' } 0.077318 {'Action Observation' }
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-0.054691 {'Memory &amp; Events' } 0.038981 {'Auditory processing' }
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-0.054037 {'Task-switching' } 0.0095692 {'Multiple Sclerosis' }
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-0.053809 {'Encoding &amp; Retrieval' } 0.008167 {'Body perception' }
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Neurosynth topics - reverse inference maps
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Test image 1
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..cs\v4-topics-100_0_stimulation_somatosensory_tms_pFgA_z_FDR_0.01.nii
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_____________________________________________________________________
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r_lowest Term_or_Topic_lowest r_highest Term_or_Topic_highest
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_________ __________________________ ___________ _____________________________
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-0.051458 {'Reading &amp; Writing' } 1 {'Sensory Stimulation' }
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-0.05124 {'Emotion face' } 0.32365 {'Pain Perception' }
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-0.049365 {'Encoding &amp; Retrieval' } 0.31546 {'Motor movements' }
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-0.0483 {'Memory &amp; Events' } 0.23224 {'Motor control' }
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-0.046738 {'Working Memory' } 0.088103 {'Action Observation' }
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-0.044211 {'Word Processing' } 0.04632 {'Motor Coordination' }
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-0.04161 {'Language comprehension'} 0.041099 {'Creativity &amp; Acupuncture '}
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-0.040511 {'Empathy &amp; Interaction' } 0.027829 {'Auditory processing' }
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-0.03783 {'Emotion Processing' } 0.016815 {'Food &amp; weight' }
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-0.031803 {'Spatial Attention' } -0.00078825 {'Multiple Sclerosis' }
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Neurosynth terms- reverse inference maps
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Test image 1
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..cs\v4-topics-100_0_stimulation_somatosensory_tms_pFgA_z_FDR_0.01.nii
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_____________________________________________________________________
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r_lowest Term_or_Topic_lowest r_highest Term_or_Topic_highest
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________ ____________________ _________ _____________________
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-0.2424 {'memory' } 0.47282 {'somatosensory'}
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-0.18946 {'retrieval'} 0.45236 {'tactile' }
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-0.18554 {'correct' } 0.42208 {'stimulation' }
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-0.18174 {'number' } 0.35855 {'hand' }
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-0.17871 {'word' } 0.32351 {'finger' }
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-0.17504 {'work' } 0.31912 {'muscle' }
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-0.16633 {'verbal' } 0.31753 {'pain' }
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-0.16625 {'face' } 0.31062 {'sensory' }
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-0.16585 {'words' } 0.30502 {'painful' }
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-0.16482 {'encoding' } 0.30338 {'sensorimotor' }
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Correlations with Yeo/Bucker resting-state networks
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Loaded images:
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/Users/f003vz1/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Combined_multiatlas_ROI_masks/rBucknerlab_7clusters_SPMAnat_Other_combined.img
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Name Pearson's r
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Visual -0.0541
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Somatomotor 0.2994
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dAttention -0.0167
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vAttention 0.0807
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Limbic -0.0438
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Frontoparietal -0.0638
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Default -0.0744
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</pre>
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<img vspace="5" hspace="5" src="canlab_help_annotate_thresholded_results_map_05.png" alt=""> <img vspace="5" hspace="5" src="canlab_help_annotate_thresholded_results_map_06.png" alt=""> <pre class="codeoutput">Prepping atlases:
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yeo17networks Loading atlas: /Users/f003vz1/Documents/GitHub/Neuroimaging_Pattern_Masks/Atlases_and_parcellations/2018_Schaefer_Yeo_multires_cortical_parcellation/Schaefer2018Cortex_17networks_atlas_object.mat
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Note: Mean weights reflect homogeneity in sign and magnitude across region,
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not high spatial frequency/pattern information.
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____________________________________________________________________________________________________________________________________________
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Wedge plot:
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Wedge plots depict mean images values across voxels. Red indicates positive values and blue negative values. If multiple images were
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entered, the darker shaded area indicates the standard error of the mean (SEM) across individuals.
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____________________________________________________________________________________________________________________________________________
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</pre>
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<img vspace="5" hspace="5" src="canlab_help_annotate_thresholded_results_map_07.png" alt=""> <p class="footer">
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<br>
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<a href="https://www.mathworks.com/products/matlab/">Published with MATLAB&reg; R2024b</a>
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<br>
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</p>
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</div>
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<!--
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##### SOURCE BEGIN #####
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%% Load a test map to use as an example
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ns = load(which('neurosynth_data_obj.mat'));
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test_map = get_wh_image(ns.topic_obj_reverseinference, 1); % somatosensory topic
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%% Run annotations
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annotate_binary_results_map(test_map)
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##### SOURCE END #####
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-->
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</body>
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</html>

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