http://gru.stanford.edu/ 2026-05-14T19:36:29-0700 http://gru.stanford.edu/ http://gru.stanford.edu/lib/tpl/gru/images/favicon.ico text/html 2025-01-28T12:34:26-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/analyses?rev=1738096466&do=diff Preprocessing analyses Preprocessing analyses are ones that create new time series. They are usually run before you run other analyses steps like correlation analysis and event-related processing. Motion Compensation Motion compensation in mrLoadRet-4.5 uses the same computational engine of mrAlign. To access the motion compensation window go to the menu: text/html 2023-12-19T15:25:56-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/atlas?rev=1703028356&do=diff Using atlas ROIs with mrTools Benson visual field atlas Running neuropythy Noah Benson has a set of python based tools that implement his method for doing surface based prediction of retinotopic visual field maps Neuropythy as well as a Bayesian analysis which combines pRF measurements with anatomical information to generate receptive field maps. text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/buglist?rev=1661892028&do=diff This page will track bugs in mrTools text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/caret?rev=1661892028&do=diff Caret Purpose The most common way to average data across subjects would be to transform all subject's functional data to a standard space (e.g., Talairach space). An alternative (and better) way to average would be to use surface-based registration, which aligns different subject's anatomy according to major landmarks of the cerebral cortex. There is a way to do this in MLR using Caret that allows users to average certain type of data (overlays, ROIs) across subjects after spherical registrati… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/checkvoxorder?rev=1661892028&do=diff Correct Order for Dimensions in the Volume Anatomies In general, if you want to check whether your volumes have the right orientation, try to load it into mlrVol. The instructions here are a bit out-of-date and specific to volume anatomies from Center for Brain Imaging at NYU and can be ignored by other users. text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/citations?rev=1661892028&do=diff How to cite mrTools Please use our Zenodo based DOI for citing use of mgl in manuscripts: The Zenodo site has a tool for how to format for different journals, but here is an example: Gardner, JL, Merriam, EP, Schluppeck, D, Besle, J, & Heeger, DJ (2018). mrTools: Analysis and visualization package for functional magnetic resonance imaging data (Version 4.7). Zenodo. text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/classificationtools?rev=1661892028&do=diff Classifier functions getInstances usage: rois = getInstances(v,rois,stimvol) purpose: compute instances by taking mean after stimulus occurrences argument value v view variable rois rois returned by loadROITSeries Optional arguments value text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/classificationtoolsnew?rev=1661892028&do=diff Typical way to do classification A typical work flow for doing classification analysis is the following: * Define some ROIs you want to use. * load the time series data for those ROIs ('loadROITSeries'). * If desired, load auxilary analysis to be used to rank voxel for feature selection (typically an event-related analysis) text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/coordinatetransforms?rev=1661892028&do=diff Coordinate Transforms Coordinate transforms lie at the heart of how MLR displays data on different base anatomies and how it keeps track of the location of ROIs. MLR coordinate transforms are based on the transformation information that is part of the $$ \left\lgroup\matrix{x_{mag}\cr y_{mag}\cr z_{mag}\cr1\cr}\right\rgroup = \left\lgroup\matrix{rs_{11}& rs_{12} &rs_{13} &t_{x_{mm}}\cr rs_{21}& rs_{22} &rs_{23} &t_{y_{mm}}\cr rs_{31}& rs_… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/documentationglm_v2?rev=1661892028&do=diff GLM statistics in mrTools This wiki page provides some more background about the v2.0 implementation of the GLM code by Julien Besle (julienbesle@gmail.com) done at Nottingham, as well as a . For the original version of the GLM analysis, on which some of the code was based, see text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/download?rev=1661892028&do=diff Download You can access an up-to-date read-only archive of mrTools using git: git clone https://github.com/justingardner/mrTools.git mrTools Once you have used checkout to get the repository, you can get updates whenever you want to by doing: git pull text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/functionreference?rev=1661892028&do=diff Function Reference This is not a complete list of functions. This contains references to some of the most useful functions in the mrLoadRet distribution. Core mrLoadRet functions mrInit usage: [sessionParams groupParams] = mrInit(<sessionParams>,<groupParams>,<justGetParams=1>,<defaultParams=1>) text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/getting_started?rev=1661892028&do=diff mrTools Getting Started text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/gettingstarted?rev=1661892028&do=diff Getting Started Add mrTools to your matlab path At the Matlab prompt, type addpath(genpath('/folderWhereYouInstalled/mrTools')) Where folderWhereYouInstalled should be replaced with the name of the folder in which you have downloaded the svn or cvs repository. text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/gui?rev=1661892028&do=diff The following are some introductory lines to the functionality of the mrLoadRet-4.5 Graphic User Interface. All options in this section will either generate a .mat file, modify mrSESSION.mat or the .img files. File Menu Look in the file menu for functions that let you load / save text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/howto?rev=1661892028&do=diff Handle not having proper Nifti format MRI data If you are using an MRI system which cannot generate correct Nifti file types with image orientation information, you may still use mrTools by Spoofing nifti xform info. Interrogate the overlay Under the Plots menu option in the text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/layeranalysis?rev=1661892028&do=diff Layer fMRI and VASO Tutorial This tutorial explains how to do layer fMRI analysis using mrTools. Much of this pipeline was developed by Renzo Huber and is described on his blog, though several steps have been adapted to mrTools. A number of software packages are required in addition to mrTools, including text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/life?rev=1661892028&do=diff Life Plugin Testing These instructions work with this dataset from Franco Pestilli. Try the directory STN/sub-FP. * Set mlrPath First make sure that you have mrTools in your path and then run mlrPath to make sure it does not conflict with vistasoft mlrPath mrTools+vista text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/mlrimage?rev=1661892028&do=diff Overview mlrImage is a set of Matlab commands that can be used for loading, manipulating, viewing and saving MRI data. These functions are intended to load, maintain and save the orientation and alignment information in the headers - particularly the text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/motex?rev=1661892028&do=diff Motex Overview Some matlab routines for downloading, processing and converting mouse GCaMP data from Benucci lab to mrTools format. Motex download Requires two repositories: * motex git clone <https://github.com/justingardner/motex.git> motex * mrTools git clone <https://github.com/justingardner/mrTools.git> mrTools Download both and add both to your Matlab path: addpath(genpath('~/proj/mrTools')) and addpath(genpath('~/proj/motex')) text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/mralign?rev=1661892028&do=diff mrAlign Getting started mrAlign is a matlab utility for aligning (or registering) MRI image volumes. We use it to align all of our data from an individual subject across scanning sessions on different days. In one scanning session, we acquire a high resolution volume anatomy. In each successive scanning session we acquire what we call text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/mrtoolssinglepage?rev=1661892028&do=diff mrTools Overview mrTools provides a set of Matlab tools to analyze fMRI data. It can do basic analyses like correlation analyses used in retinotopy experiments, event-related, population RF and GLM analyses. It can display the results of analyses on inplane anatomies, flat maps and surfaces. It is designed to make it easy to write your own script and programs in Matlab to analyze your data. text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/my_first_analyses_a_cookbook?rev=1661892028&do=diff This tutorial assumes familiarity with MatLab. It also assumes that you have your data reconstructed by the CBI-functions and they are saved in the heegerlab directory under your name. It might also be helpful to download and go through all 3 tutorials on the lab-wiki to get to terms with the different programs a little before starting. text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/overview?rev=1661892028&do=diff mrTools Overview mrTools provides a set of Matlab tools to analyze fMRI data. It can do basic analyses like correlation analyses used in retinotopy experiments, event-related, population RF and GLM analyses. It can display the results of analyses on inplane anatomies, flat maps and surfaces. It is designed to make it easy to write your own script and programs in Matlab to analyze your data. See text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/plugins?rev=1661892028&do=diff Plugins Overview You can add plugins to the MLR interface that allow for additional customized menu items, colormaps and interrogators. Plugins can also change the functionality of user interface items (by installing their own callbacks to existing text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/q-form?rev=1661892028&do=diff The Q form and S form of a canonical volume should be the same. It is not important for it to be exact, but it has to be basically correct, so you can initialize alignments. For volumes recorded on our magnet, a serviceable Q = S form is: 0.9994 -0.0349 0.0000 -81.5687 0.0349 0.9994 0.0000 -131.4221 -0.0000 -0.0000 1.0000 -132.7831 0 0 0 1.0000 text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/scripting?rev=1661892028&do=diff Example function illustrating how to access data with viewGet/viewSet This is a simple example to illustrate how to write your own custom 'analysis' code and functions to integrate with mrTools-4.5. The function writes an animated gif file that shows the mean or median fMRI/EPI data over time in false color, superimposed on your inplane anatomies. Not particularly life-changing, but quite useful for (1) inspecting whether you inplane anatomies and EPI data are aligned (2) how bad distortions o… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/scriptinganalyses?rev=1661892028&do=diff Writing Analyses mrLoadRet is designed to make it relatively easy to write an entirely new data analysis stream. The quickest way to do this is to script it and use mrDispOverlay to display the results. A complete implementation that is fully integrated with the mrLoadRet text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/scriptingexamples?rev=1661892028&do=diff mrTools Scripting Examples * Retinotopy * Event Related * Creating an animating GIF text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/scriptingexamplesanimatinggif?rev=1661892028&do=diff Creating an animating GIF This is a simple example to illustrate how to write your own custom 'analysis' code and functions to integrate with mrTools-4.5. The function writes an animated gif file that shows the mean or median fMRI/EPI data over time in false color, superimposed on your inplane anatomies. Not particularly life-changing, but quite useful for (0) learning how to get started coding, (1) inspecting whether you inplane anatomies and EPI data are aligned (2) how bad distortions of the… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/scriptingexampleseventrelated?rev=1661892028&do=diff Event Related Tutorial (scripting) This shows you had to do all the analysis form the Event Related Tutorial without the GUI. Note that you may also want to set your verbose setting in Edit/Preferences to 'No' so that all messages and waitbars get printed out at the command line rather that in a dialog. text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/scriptingexamplesretinotopy?rev=1661892028&do=diff Retinotopy Tutorial (Scripting) This page show how the analysis steps done in the Retinotopy tutorial can be scripted without any GUI interaction. If you don't know how to run a retinotopy analysis with the GUI then you should go through the Retinotopy tutorial. Overview text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/scriptingexamplesxform?rev=1661892028&do=diff Transforming data across scans/sessions mrLoadRet has been written to make it relatively easy to combine data sets that have been acquired with different different slice prescriptions (and/or different voxel sizes). Sometimes this is done within the same scanning session but more frequently it is because data from the same subject were acquired in separate scanning sessions. text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/scriptingoverview?rev=1661892028&do=diff Scripting Overview Everything can be scripted in MLR without any interaction with the GUI. Scripting can be as simple as writing a quick function to perform all the analysis steps that you typically run on a retinotopy experiment or your event-related experiment. In other cases, scripting may be the way that you run a much more complex analysis like fully analyzing an adaptation experiment or a classification experiment. The goal of MLR is to make these tasks easy by providing a Matlab interfac… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/spoofxforms?rev=1661892028&do=diff Overview If you do not have orientation information for your MRI data (for example if you do not have your data in Nifti format) you may still use MLR. But, you will need to manually set the orientation information - here are some steps for how to do this. This assumes that you have a text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/surfacesandflatmaps?rev=1661892028&do=diff Surfaces and Flat Maps This section will give you an overview of how surfaces and flat maps work in MLR. You may wish to start by going through the Surfaces and Flat Maps Tutorial before going through this page. It is important to note that MLR is not a tool for segmenting 3D volumes and generating surfaces. You can use any tool that is capable of generating an outer (pial) surface and inner (boundary between gray and white matter) surface. If you have these two files, then you will be able to… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/tailarach?rev=1661892028&do=diff The link you clicked should have brought you here text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/talairach?rev=1661892028&do=diff Talairach If a base anatomy has a Talairach transformation assigned to it, mrTools will display Talairach coordinates when that base is being viewed. In addition, any ROIs defined on a base with Talairach can be aligned to ROIs from any other brain, on the basis of the Talairach values. mrTools does all of this automatically, and gives specific warnings and instructions so that you are aware if this is happening. text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/talairachcoordinates?rev=1661892028&do=diff Using Talairach Coordinates with mrLoadRet Overview The way we've implemented the use of registration to the Talairach coordinate system is by keeping track of a single transform. We don't currently support anything other than a single transformation of the whole brain. Once a transform is defined for a given brain, (see below) it can be saved to the base volume for that brain and then it will be inherited by everything aligned to or defined on that base volume. In this way, scans and ROIs fro… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/talequation?rev=1661892028&do=diff Calculating the transformation matrix, from the points chosen by the user How the 4x4 transform, saved as base.vol2tal, is calculated We calculate the 4×4 transform that takes the volume from the original coordinates to talairach coordinates. This transform is never actually applied to the volume. Rather, it is saved (in the base structure, as base.vol2tal), and used in calculations, both to display Talairach coordinates when viewing the volume on mrLoadRet, and to align ROIs across different … text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/todo?rev=1661892028&do=diff * add necessary viewSet / viewGet calls so that you never need to dereference the MLR structure. * viewGet(v, 'glmBetas') * text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/top?rev=1661892028&do=diff mrTools * Overview * Download * Getting Started * Tutorials * Retinotopy * Event Related * Surfaces and Flat Maps * General Linear Model * Population RF * Classification * My first Analyses, a cookbook * GUI * Analyses * Coordinate Transforms * Assigning Talairach transform * Surfaces and Flat Maps * Caret * Scripting * Overview * Examples * Retinotopy * Event Related * Creating an animating GIF * Transforming data across scans/sessions * Writi… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/troubleshooting?rev=1661892028&do=diff Troubleshooting Indexing When scripting your own analysis code, you should watch out for the following thing: Let's say there are several scans in the group you're analyzing (for the sake of illustration, let's say there are 10 scans in the group). And let's say you only want to analyze a subset of those scans (because you've already done the analysis on some of the scans, or because some of the scans shouldn't be analyzed this way) - for the sake of illustration, let's say scans 2, 5 and 9. T… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/tutorialsclassify?rev=1661892028&do=diff Classification tutorial overview This tutorial explains classification analysis with fMRI data using mrTools. Classification analysis can be used to examine distributed patterns of activity - often subtle responses that are hard to examine with other methods. For example, the responses to different orientations which might be distributed across the cortex (see: text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/tutorialseventrelated?rev=1661892028&do=diff Event Related Tutorial This tutorial will show you how to run an event-related analysis. Note that the Retinotopy Tutorial is the best place to start for a full introduction to using mrLoadRet. This tutorial starts after the initial steps of running mrInit, the Motion Compensation and Alignment text/html 2023-09-27T14:17:11-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/tutorialsglm_v2?rev=1695849431&do=diff GLM Tutorial This tutorial shows you how to run a single-subject GLM analysis with mrLoadRet. The General(ized) Linear Model is commonly used for fMRI data analysis. Basically it is an analysis in which you specify a set of factors that you think will have influenced the time series of your fMRI data and assume that these factors all sum linearly with an unknown weighting (i.e. beta weight) for each voxel. Each factor is really just a vector of 1's and 0's specifying when an event of a particul… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/tutorialspopulationanalysis?rev=1661892028&do=diff pRF Analysis Tutorial This tutorial shows you how to run a population analysis with mrLoadRet. It is a good place to start if you are just learning how to use mrLoadRet. Overview * Download the tutorial files * The stimuli used in the experiment text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/tutorialsprf?rev=1661892028&do=diff pRF Tutorial This tutorial shows you how to run a pRF analysis (see Dumoulin and Wandell (2008) for details - also Kay, Naselaris, Prenger and Gallant (2008)) with mrTools. The basic idea of a pRF analysis is to fit a “population receptive field” to each voxel. This is usually based on stimuli similar to a typical retinotopy experiment (rotating wedges, rings and moving bars). The responses to these stimuli are predicted by a very simple gaussian receptive field model. The gaussian RF has param… text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/tutorialsretinotopy?rev=1661892028&do=diff Retinotopy Tutorial This tutorial shows you how to run a retinotopy analysis with mrLoadRet. It is a good place to start if you are just learning how to use mrLoadRet. Overview * Download the tutorial files * The stimuli used in the experiment text/html 2022-08-30T13:40:28-0700 Anonymous (anonymous@undisclosed.example.com) http://gru.stanford.edu/doku.php/mrtools/tutorialssurfacesandflatmaps?rev=1661892028&do=diff Surfaces and Flat Maps Tutorial This tutorial will show you how to import a surface segmentation into mrLoadRet so that you can view your data on a surface. It will also show you how to make a flat map from that surface. Overview * Download tutorial data