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plugins and d15 script for extracting and plotting nps subregions from second level DAT object
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‎Second_level_analysis_template_scripts/core_scripts_to_run_without_modifying/d15_plot_local_nps_responses_by_region.m‎

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%% Extract and Plot all NPS sub regions
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% Once the CANlab second level batch prep_* sequence has been run, this
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% script will identify all NPS subregions in the DAT object and then
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% extract and plot those subregions one by one. Figures will automatically
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% be saved in the figsavedir, which is set in a_set_up_paths_always_run_first.m
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% get list of all NPS sub regions
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regions = cat(2, DAT.NPSsubregions.posnames, DAT.NPSsubregions.negnames)
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% Loop through DAT object and for each NPS sub region, extract data and
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% plot
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for i=1:length(regions)
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nps_local_object = plugin_extract_local_nps_region_vals(DAT, regions{i});
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plugin_plot_local_nps_region_vals(nps_local_object, figsavedir);
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end

‎Second_level_analysis_template_scripts/core_scripts_to_run_without_modifying/plugin_extract_local_nps_region_vals.m‎

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function NPS_region_vals = plugin_extract_local_nps_region_vals(second_level_DAT_object, my_region)
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%% Helper function to extract local NPS region values from DAT object
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%
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%
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% This program is free software: you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as published by
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% the Free Software Foundation, either version 3 of the License, or
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% (at your option) any later version.
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%
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% This program is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License
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% along with this program. If not, see <http://www.gnu.org/licenses/>.
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% ..
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%
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% :Usage:
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% ::
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% **NOTE**: This script and it's counterpart,
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% plugin_plot_local_nps_region_vals.m, ONLY pertain to the CANlab 2nd level
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% script system. They are not for general use. The input data object
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% for this script is a DAT object, which is specific to the 2nd level
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% script system, and other data objects may not work as intended with
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% this function.
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%
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%
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% NPS_region_vals = extract_local_nps_region_vals(second_level_DAT_object, nps_region_of_interest)
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%
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%
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% :Inputs:
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% 1.) An CANlab 2nd level batch script DAT object: This is most likely created by using the
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% canlab 2nd level scripts, which can create a DAT object with the
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% property NPSsubregions. This function will use this property to extract
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% relevant data.
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%
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% 2.) An NPS region of interest: This can be any of the positive or
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% negative regions of the NPS, which include:
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%
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% posnames: {'vermis' 'rIns' 'rV1' 'rThal' 'lIns' 'rdpInsDATA_STRUCT' 'rS2_Op' 'dACC'}
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% negnames: {'rLOC' 'lLOC' 'rpLOC' 'pgACC' 'lSTS' 'rIPL' 'PCC'}
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%
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% :Outputs:
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% 1.) NPS_region_vals: A data structure with the following properties
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% A.) Region: This is the NPS region from which the function is extracting data
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% B.) condition_data: Values from input fmri_data_object
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% (usually DAT from 2nd level analysis) that correspond to NPS activation
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% in input my_region. Values grouped by conditions in input fmri_data_object.
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% This function pulls from fmri_data_object.NPSsubregions
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% C.) condition_names: Names of conditions from
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% fmri_data_object (usually DAT from 2nd level analysis) that
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% describe the condition_data groups. This function pulls from input
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% fmri_data_object.conditions
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% D.) contrast_data: Values from input fmri_data_object
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% (usually DAT from 2nd level analysis) that correspond to NPS activation
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% in input my_region. Values grouped by contrasts in input fmri_data_object.
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% This function pulls from fmri_data_object.NPSsubregions
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% E.) contrast_names: Names of contrasts from fmri_data_object
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% (usually DAT from 2nd level analysis) that describe the
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% contrast_data groups. This function pulls from input
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% fmri_data_object.contrastnames
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% F.) colors: Colors pulled from input fmri_data_object for plotting
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% by conditions
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% G.) contrast_colors: Colors pulled from input fmri_data_object for
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% plotting by contrasts
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% :Examples:
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% (1) NPS_region_vals = extract_local_nps_region_vals(DAT, 'dACC') %saves dACC
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% values to new variable NPS_region_vals
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%
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% (2)To load in a CANlab second-level analysis session, extract an NPS subregion, and
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% then plot it by condition/contrast:
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%
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% %reload second level analysis objects
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% addpath(genpath('/path/to/data/files'));
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% a_set_up_paths_always_run_first;
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% b_reload_saved_matfiles
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%
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% %Example to extract dACC from DAT
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% NPS_local_dACC = extract_local_nps_region_vals(DAT, 'dACC')
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%
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% %Example to plot newly extrated dACC object
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% plot_local_nps_region_vals(NPS_local_dACC)
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% Get INPUTS
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region = my_region;
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in_DAT = second_level_DAT_object;
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% check input region and designate pos or neg NPS
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if sum(strcmp(in_DAT.NPSsubregions.posnames, region)) == 1
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pos_or_neg_field = 'npspos_by_region'; % set flag field to positive
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wh_region = strcmp(in_DAT.NPSsubregions.posnames, region); % find index of input region
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sprintf('Input region %s is an NPS Pos region.', region)
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elseif sum(strcmp(in_DAT.NPSsubregions.negnames, region)) == 1
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pos_or_neg_field = 'npsneg_by_region'; % set flag field to negative
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wh_region = strcmp(in_DAT.NPSsubregions.negnames, region); % find index of input region
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sprintf('Input region %s is an NPS Neg region.', region)
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else
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error('Bad Region Name')
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end
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% Check input data for specified region for each condition
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region_index = find(wh_region);
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for i = 1:length(in_DAT.NPSsubregions.(pos_or_neg_field))
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if size(in_DAT.NPSsubregions.npspos_by_region{i}, 2) < region_index
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warning('Input object does not have NPS Data for specified region for every condition')
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end
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NPS_region_vals = [];
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NPS_region_vals.region = region;
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k = length(in_DAT.conditions);
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kc = length(in_DAT.contrastnames);
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% check for problems
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if sum(wh_region) > 1 || sum(wh_region) == 0, error('Bad region name'); end
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% get the condition data
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NPS_region_vals.condition_data = cell(1, k);
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NPS_region_vals.conditions = in_DAT.conditions;
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for i = 1:k
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NPS_region_vals.condition_data{i} = in_DAT.NPSsubregions.(pos_or_neg_field){i}(:, wh_region);
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end
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% get the contrast data
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NPS_region_vals.contrastnames = in_DAT.contrastnames;
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myfield = [pos_or_neg_field '_contrasts'];
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for i = 1:kc
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NPS_region_vals.contrast_data{i} = in_DAT.NPSsubregions.(myfield){i}(:, wh_region);
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end
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% Copy colors for use later in plotting
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NPS_region_vals.colors = in_DAT.colors;
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NPS_region_vals.contrastcolors = in_DAT.contrastcolors;
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end

‎Second_level_analysis_template_scripts/core_scripts_to_run_without_modifying/plugin_plot_local_nps_region_vals.m‎

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function plugin_plot_local_nps_region_vals(nps_region_extract, save_dir)
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%% Helper function to visualize local NPS region values from nps region extract (can be created by extract_local_nps_region_vals.m).
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%
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%
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% This program is free software: you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as published by
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% the Free Software Foundation, either version 3 of the License, or
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% (at your option) any later version.
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%
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% This program is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License
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% along with this program. If not, see <http://www.gnu.org/licenses/>.
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%
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%
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% :Usage:
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%
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% **NOTE**: This script and it's counterpart,
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% plugin_extract_local_nps_region_vals.m, ONLY pertain to the CANlab 2nd level
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% script system. They are not for general use. The input data object
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% for this script is a DAT object, which is specific to the 2nd level
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% script system, and other data objects may not work as intended with
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% this function.
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%
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% plot_local_nps_region_vals(NPS_region_values_object)
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%
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%
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% :Inputs:
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% 1.) An NPS_region_vals data object: This should be a data object including only
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% data from one NPS subregion. This object can be created using the
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% extract_local_nps_region_vals.m on a CANlab second level scripts DAT
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% object.
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%
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% :Outputs:
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% 1.) Two plots: One of the data from the NPS subregion of interest by
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% condition and one by contrast.
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%
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% :Examples:
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% (1) plot_local_nps_region_vals(NPS_region_vals)
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%
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% (2) To load in a CANlab second-level analysis session, extract an NPS subregion, and
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% then plot it by condition/contrast:
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%
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% %reload second level analysis objects
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% addpath(genpath('/path/to/data/files'));
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% a_set_up_paths_always_run_first;
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% b_reload_saved_matfiles
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%
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% %Example to extract dACC from DAT
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% NPS_local_dACC = extract_local_nps_region_vals(DAT, 'dACC')
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%
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% %Example to plot newly extrated dACC object
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% plot_local_nps_region_vals(NPS_local_dACC)
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% Get input data
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DATA_STRUCT = nps_region_extract;
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num_cond = length(DATA_STRUCT.conditions); % get number of conditions
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num_cont = length(DATA_STRUCT.contrastnames); % get number of contrasts
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empty_conditions = cell(1,num_cond); % set condition names to empty string to plot clear x-axis
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empty_contrasts = cell(1,num_cont); % set contrast names to empty string to plot clear x-axis
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% Create empty plot
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f1 = create_figure(DATA_STRUCT.region, 1, 2);
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% Get condition data and specify options to be plotted
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mydata = DATA_STRUCT.condition_data;
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input_options = {'colors', DATA_STRUCT.colors, 'nofig', 'names', empty_conditions, 'noviolin', 'noind'};
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% Plot condition data
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barplot_columns(mydata, input_options{:});
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% Populate labels for conditions plot
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%title('Conditions');
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%ylabel(sprintf('%s local pattern response', DATA_STRUCT.region));
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xlabel(sprintf(''));
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ylabel(sprintf(''));
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subplot(1, 2, 2);
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% Get contrast data and specify options for plotting
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mydata = DATA_STRUCT.contrast_data;
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input_options = {'colors', DATA_STRUCT.contrastcolors, 'nofig', 'names', empty_contrasts, 'noviolin', 'noind'};
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% Plot contrast data
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barplot_columns(mydata, input_options{:});
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% Populate labels for contrasts plot
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%title('Contrasts');
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%ylabel(sprintf('%s local pattern response', DATA_STRUCT.region));
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xlabel(sprintf(''));
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ylabel(sprintf(''));
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%save output as Support vector graphics file image (SVG)
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print(f1, [save_dir '/' DATA_STRUCT.region '_condition_contrast_plot'] , '-dsvg');
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close all;
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clear f1;
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sprintf('Image %s _condition_contrast_plot.svg was saved to: \n %s', DATA_STRUCT.region, save_dir)
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end

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