Scripts to reproduce the analysis described by Rebollo et al on stomach brain synchronisation
General organization of scripts:
The scripts are organized according to prefixes
Global scripts: Global variables, like subject indexes, path, filenames MRI scripts: Preprocessing of mri antomical and functional images using SPM8 Prepro scripts: preprocessing of the EGG inside and outside the scanner timeseries scripts: Analysis of BOLD and EGG timeseries, estimation of chance and empirical PLV, group level statistics Tools scripts: bandpass filter, brain atlas lookup, write mri, vox2mni,mni2vox Network scripts: Coherence and phase angle analysis of gastric network Paper scripts: Scripts to make specific analysis for figures for the paper
The main script is paper_main, from which all the analysis can be launched. All analysis were performed with Matlab 2013 (and SPM 8) except one step of fMRI preprocessing, documented in paper_main
Global scripts global_path2root path to Physiens root folder
global_path2subject path to subject specific folder
global_filename Function that defines the path of all files in PHYSIENS study by concatenating the different elements composing the path and filename. The output of the function is a string containing the complete path to the requested file that can be used to load the file
Global_subjectList List of all artifact free subjects included on PHYSIENS final analysis
global_getcfgmain Function defining a matlab structure containing the final parameters used through the preprocessing and analysis pipeline. This structure is a mandatory input to most PHYSIENS functions, either to know which parameter apply or which filename retrieve/store using global_filename. In order to retrieve the path to a file, the different parts of the cfgMain structure are concatenated when calling global_filename
global_getEGGpeaks Load the file containing the channel number and exact frequency for all subjects during the fMRI acquisition, which was manually estimated in the first call of prepro_egg and stored in the log file together with the EGG phase timeseries in each subject timeseries folder. The file to be loaded was created by the function prepro_egg_saveChannelInfo
global_getEGGpeaksOutsideScanner Retrieve the frequency of the EGG peak recorded when subjects where outside the scanner in order to do the analysis performed in paper_controlPeaksOustideScanner
global_getGastricNetwork Retrieves and load the mask of the gastric network obtained from 30 subjects.
MRI MRI scripts are run with matlab 2011 and SPM8. These scripts needs the functions in the folder MRITools
MRI_group_preproc
Toplevel batch for preprocessing with SPM8 by Anne-Dominique Lodeho. To use this batch, please edit the beginning of this file and run it. you need to specify which particular tasks to perform, through the TODO structure with binary fields (1|0): todo.slice_timing = 1; todo.realign = 1; todo.normalize = 1; todo.coregister = 1; todo.apply_norm = 1; todo.smooth = 1; todo.run = 1; This functions iterates through subjects and calls MRI_single_preproc that does the actual call to SPM
MRI_single_preproc Create an SPM8 job for single subject's preprocessing by Anne-Dominique Lodeho with the parameters specified in MRI_group_preproc
Prepro scripts Prepro_egg Basic preprocessing steps for obtaining and storing the EGG phase per mri volume
prepro_egg_loadData Function to retrieve subject EGG and IRM volume markers recorded inside or outside the scanner. This function is called by prepro_egg
prepro_egg_path2data This function get the full path of different kind of files, e.g. brainamp markers, for a particular subject. This function is called by prepro_egg_loadData
prepro_egg_downsampleMarkers Get closest sample number of new marker based on the timestamps of the not downsampled data
prepro_egg_saveChannelInfo Create a file in the folder scripts/files called EGG_peaks_info based on the log of the preprocessing of each subject, it retrieves the mostpowerfull frequency and channel of each subject and put it on a table. The original selection of channels and frequency peaks is done on the first call to prepro_egg, with the paramter cfgMain.automaticChannelSelection == 0
prepro_egg_outsideScanner Similar to prepro_egg buy preprocess the brainamp files containing the EGG recorded outside the scanner.
timeseries scripts timeseries_prepare_import2matlab Construct fMRI timeseries (time,voxels) from swaf images located at each subject folder and saves them as a structure in the HDD.
timeseries_preprocessBOLD Takes the output of timeseries_prepare_import2matlab that is stored in each subject timeseries\data folder and preprocess it so it can be further analyzed Preprocessing steps, implemented in fieldtrip, includes remove polinomial trends of second degree, bandpass filter between 0.01 and 0.1 Hz and standarize to Z units the output is stored in the tiemseries folder of each subject
timeseries_csfSignal_obtainAndRegress This function retrieves the timeseries of a 3x3 cube of voxels located in the CSF and regress it out the of all the brain voxels, the timeseries, the residuals of the regression and the betas coefficient are all stores in the timeseries folder of each subject.
timeseries_preparePhases_Regression Load EGG and FMRI timeseries, filter fMRI timeseries at gastric peak, extract phases of fmri timeseries(CSFregressed) and save them into disk in timeseries folder.
timeseries_mapPLV_Regression Computes and store in timeseries/data folder a 3D nifti volume with phase locking value between the EGG and each voxel timeseries
timeseries_medianRotation_Regression Stores a .nii image of the median PLV obtained with a timeshifted EGG signals concatenated and rotated). It does all 360 possible rotations of EGG signal and calculate PLV at each rotations and takes the median PLV obtained across timeshift across voxels to be used as surrogate PLV in group level statistics
timeseries_AllRotations_Regression Stores a matlab file with the PLV obtained from all 360 possible rotations of EGG signal. The file is later used in the false positive rate control script paper_control_randomziationTimeShifts
timeseries_statsCluster_Regression Perform group level statistics comparing empirical versus chance PLV by using the clustering randomization procedure provided by fieldtrip (Maris and Oostenveld 2007)
timeseries_FWD_BOLD_GLM Store the timeseries of absolute derivative of movement (separately for rotation and translations) i.e. Framewise displacement. Then compute the GLM between the BOLD timeseries and the framewise displacement. To be later used by the script paper_control_corrMovement_CS.Store figure into disk for each subject. Networks scripts networks_coherence_getClustertimeseries Compute and stores the average BOLD time series across each significant cluster of the gastric network. Later used for coherence and angle analysis.
networks_coherence_getFullBandEGG Compute and stores the fullband (0.01-0.10 EGG time series in order to compute coherence with the BOLD signal in significant clusters.
networks_coherence_getCoherence This function computes the coherence between the EGG and all gastric network regions and between all gastric network regions for a given participant and store it into disk networks_coherence_group This Script loads the BOLD-EGG coherence values of all subjects in a loop and average them at gastric peaking frequency separately for each subject. The resulting values are used in table 1 of the paper
networks_coherence_main Simple script that calls the relevant functions to perform the coherence analysis between gastric network and the EGG at the group level.
networks_couplingStrenght_obtain Computes difference between median and empirical PLV (coupling strength) and stores in the HDD. These values are later used in the control with head micro movements
networks_phaseAngle_obtain This function 1 Loads cluster timeseries for each subject and EGG 2 Get angle and value of phase locking for each cluster 3 Subtract mean phase across clusters to the angle of each cluster 4 Plots previous steps and store them into HDD 5 Stores the angle and magnitude of PLV for each cluster
networks_phaseAngle This scripts loads the angle of phase locking of each cluster and subject, average them, perform the watson-william statistical test, plot them, and store them in nifti format (Figure 4 of the paper).
Paper scripts paper_controlPeaksOustideScanner Control to check if the EGG peaks are the same inside and outside the scanner. First calls prepro_egg_outsideScanner to preprocess EGG outside the scaner. Manual corrections in 4 subjects is applied. Then perform a ttest between peaks inside and outside the scanner.
paper_MakeTable1 The output of this function is used in table 1 of the paper to identify the regions belonging to the gastric network using automatic anatomical labeling(AAL). Input: cfgMain structure used to obtain results, which allows to load the group level masks. The output is the area number, the number and volume of voxels in that area, the percentage of the area in the cluster, the tvalue at peak coordinates and the x y z MNI coordinates of the peak
paper_controlOffset_MAIN Perform filter offset control. Filters BOLD and EGG timeseries with frequency offsets from the EGGpeak in steps of 0.001 Hz, calculates empirical and chance PLV and performs group level statistics. It then loads the group level stats of all offsets and plots them to be used in figure 2B Modifying the parameter cfgMain.offset changes the filenames of all relevant files when calling global_filename in order to reflect the desired filter offset.
paper_ROIinsula Perform analysis presented in section: Sub-threshold coupling in the right posterior insula Load Deen 2011 parcellation of right and left anterior, posterior and middle insula. Compute for each subject average BOLD time-series in each of these ROIs, calculate empirical and chance and perform a ttest comparing them.
Paper_ComparisonSharedVariance This script produces the analysis presented in figure 4D It compares the estimates of functional connectivity (shared variance) between gastric, saliency and default regions using coherence and correlations It thens plots the timeseries of an exempe subject.
Paper_ComparisonSharedVarianceAllNodes This scripts compares estimates of shared variance between all nodes of the gastric network using the squared coherence and squared correlation coefficient. It then performs a ttest to check for significant differences. The resulting values are reported in the text of the paper, section 'Temporal advances and lags in the gastric network '.
paper_control_corrMovement_CS Perform correlation between the framewise displacement betas and coupling Strength in all voxels of the gastric network. Reported in section Gastric-coupling in gastric network is not related to head micromovements
paper_bayes_MAIN Compute Bayes Factor for the influence of different variables on gastric-BOLD coupling strength 1- Framewise displacement, one sample ttest 2- EGG power, frequency, traitAnxiety, BMI. Correlation 3- Gender, two sample ttest
paper_quantifyAutonomicOverlap This script quantify the overlap between voxels of the gastric network and the electrodermal activity related regions provided by Beisnner 2013.
paper_randomization_createRandomizationMatrix Creates and saves a matrix defining the time-shifts that will be used for each subject at each iteration for the randomization control. To call only once, and then load the output matrix stored in Y:\scripts\files\randomizationRotationMatrix
paper_randomization_randomize This script performs the group level statistics with PLV obtained with random timeshifts to the EGG timeseries across subjects. The PLV obtained with all possible timeshifts is obtained with randomization of EGG phases using the script timeseries_AllRotations_Regression The randomization matrix is loaded, which contains for each iteration (1:1000), which PLV of time-shifted EGG (out of 360), will be assigned to each of the 30 subjects It then calls paper_randomization_statsCluster to perform group level statistics on these surragate data.
paper_randomization_statsCluster This script performs the group level statistics for the randomization control. Instead of comparing the median rotation PLV against the empirical PLV, it compares the median rotation PLV against a random rotation, which is previously determined in the file Y:\scripts\files\randomizationRotationMatrix
paper_randomization_figure
Tools scripts tools_get_indexBrain Get index of voxel outside/inside brain in vector format based on SPM apriori mask
tools_bpFilter Forward and reverse filter the signal using filtfilt. This corrects for phase distortion introduced by a one-pass filter. filterType has to be specified as string input e.g. ’fir2’
tools_vox2mni Voxel space to MNI space
tools_mni2vox MNI space to Voxel space
tools_writeMri Write 3d or 4d data in nifti file using fieldtrip