https://neuroelf.com/wiki/ 2026-04-14T14:12:14+00:00 https://neuroelf.com/wiki/ https://neuroelf.com/wiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2010-06-21T05:40:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=acq.channeldata&rev=1277098836&do=diff ACQ::ChannelData - access channel data in raw sampling frequency Motivation Different object types have different field names/properties and/or store the underlying data differently (e.g. in a samples-by-channel table or in different fields). This method (which is available also for the text/html 2010-06-22T21:21:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=acsvread&rev=1277241683&do=diff acsvread Motivation Very frequently data analysis is performed using several different programs at a time (e.g. Excel for text file pre-processing, Matlab for fMRI data analysis and R/SAS/SPSS for specific group statistic models), which leads to the question of how to best transfer data between programs. text/html 2011-04-05T03:48:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=adding_articles&rev=1301975333&do=diff wiki internals - adding articles Motivation The information accessible at this site should be comprehensive and well structured. To achieve this, a basic structure for each article is desired. Requirements Please think about what information you would like to convey, and as a first step, answer the following questions: text/html 2010-05-26T04:35:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=alphasim_-_extended_uses&rev=1274848518&do=diff alphasim - extended uses Motivation Under certain circumstances, the traditional way to employ alphasim does not provide the user with the appropriate cluster-level thresholds to actually correctly achieve the desired false-positive rate (of maps, FWE/Bonferroni-corrected alpha level): text/html 2010-06-22T03:28:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=analyzetype&rev=1277177325&do=diff analyzetype (reference only) analyzetype - return properties of analyze image datatype FORMAT: [anadata, anareadtype, anareadsize] = analyzetype(anatype) Input fields: anatype numeric datatype given in Analyze header Output fields: anadata 1x1 data field with correct type and zero content anareadtype type string for fread operations anareadsize number of bytes per pixel/voxel text/html 2011-04-04T15:32:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=attaching_a_protocol_to_a_vtc&rev=1301931156&do=diff Attaching a protocol to a VTC Motivation BrainVoyager QX uses the name of a “linked protocol file” from the VTC header for quite a few built-in functions (e.g. when visualizing the conditions as colored background patches from the protocol information when displaying time courses). text/html 2010-06-22T16:01:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=binread&rev=1277222514&do=diff binread (reference only) binread - reads a binary into one uint8 array FORMAT: bincont = binread(filename) Input fields: filename name to a file, preferably absolute path Output fields: bincont 1xN uint8 array See also asciiread, binwrite text/html 2010-06-22T16:05:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=binwrite&rev=1277222719&do=diff binwrite (reference only) binwrite - writes a binary stream from a char/uint8 array to file FORMAT: binwrite(filename,content) Input Fields: filename name to a file, preferably absolute path content char/uint8 array to write See also asciiwrite text/html 2011-03-31T18:21:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=bvqxfile&rev=1301595715&do=diff BVQXfile Motivation Given that this toolbox is the successor of BVQXtools (a toolbox solely meant for BrainVoyager QX file formats), the function to perform file I/O was renamed. To be able to continue using older scripts that were written with BVQXtools (using a class named BVQXfile), this function is provided as a transparent pass-through function. text/html 2010-06-22T02:41:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=checking_xff_files_for_problems&rev=1277174500&do=diff Checking xff files for problems Motivation While the xff class and methods provide a convenient interface, the code is somewhat hidden behind the subsref and subsasgn overloading mechanism in Matlab. This can make it more difficult to find out why any given file might produce an error message. text/html 2011-04-28T16:37:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=close_neuroelf_gui_after_clear_classes&rev=1304008623&do=diff How to close the NeuroElf GUI after clearing everything Motivation Sometimes you accidentally enter clear classes which then, inadvertently, also clears the contents of all displayed objects, which makes Matlab (due to the GUI's callbacks) go haywire and spit out tons of errors and warnings. text/html 2010-06-22T03:21:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=colcode2uint32&rev=1277176877&do=diff colcode2uint32 (reference only) colcode2uint32 - convert from colcode to uint32 array FORMAT: outarray = colcode2uint32(inarray) Input fields: inarray Nx4 input array of type colcolde (n, 1) = color index or NaN (n, 2) = red component (0...255) (n, 3) = green component (0...255) (n, 4) = blue component (0...255) Output fields: outarray Nx1 uint32 array See also uin… text/html 2010-06-22T03:44:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=colorpicker&rev=1277178299&do=diff colorpicker Motivation As part of a toolbox with a GUI that supports statistical map overlay, I wanted to have a nice interface to select (pick) colors. Most programs (e.g. Photoshop) have a comparable option. Function reference ('help colorpicker') text/html 2010-06-22T21:20:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=computehrv&rev=1277241601&do=diff computehrv Motivation Both heart beat onsets (R wave time points) as well as sliding beats-per-minute (BPM) are already interesting measures, but most publications refer to summary measures when GCR data reported. One of the most common of these is heart-rate variability (HRV). This function computes the power spectral contribution of frequencies in two specified ranges. text/html 2010-06-22T03:10:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=convones&rev=1277176239&do=diff convones Motivation The main motivation to use convones is to have a faster routine for the special case where one of the arguments of a one-dimensional convolution is a series of all-1 values. Reference convones - convoles a function with a number of consecutive ones FORMAT: cfunc = convones(f, cnum [, w]) Input fields: f function to convolve cnum number of consecutive ones to use w if 1x1 true, weight (divide by number o… text/html 2010-06-25T18:48:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=creating_and_combining_masks_from_vtcs&rev=1277491713&do=diff Creating and combining masks from VTCs Motivation I wanted to create this page for two reasons: * demonstrate quickly the ease of access on xff objects (in this case BrainVoyager QX types) * give users the ability to create an SPM-comparable mask when running GLMs text/html 2011-04-05T03:51:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=creating_formula_images&rev=1301975482&do=diff Creating formula images Motivation Many concepts in neuroscience can be condensed into a (series of) mathematical equation(s). A prominent example is the ordinary least-squares multiple regression case, which uses the outcome of the matrix inversion of the covariance matrix of the design: text/html 2011-04-14T18:03:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=dcm2nii&rev=1302804238&do=diff dcm2nii (import DICOM images using SPM's DICOM Import) Motivation Neuroimaging data is usually acquired in a format unsuitable for data processing (e.g. missing or incomplete support for data manipulation in existing files), such as DICOM or PAR/REC (Philips proprietary). SPM comes with an import function for this, and the dcm2nii function collects the required information and passes it on to the SPM Job manager. text/html 2011-04-14T18:15:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=dicom2nii&rev=1302804959&do=diff dicom2nii (import DICOM or PAR/REC images) Motivation Neuroimaging data is usually acquired in a format unsuitable for data processing (e.g. missing or incomplete support for data manipulation in existing files), such as DICOM or PAR/REC (Philips proprietary). For those who do not have SPM available but still want to be able to convert DICOM or PAR/REC images, NeuroElf also offers an experimental function that converts from those formats into 3D/4D NIftI files. text/html 2010-06-23T05:17:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=displaying_the_motion-parameters_of_a_subject&rev=1277270252&do=diff Displaying the motion-parameters of a subject Motivation While SPM writes out the motion parameters into a text file, sometimes only the files remain (e.g. after pruning the folders). For such cases, the motion parameters can be retrieved from the Analyze files and re-displayed using the text/html 2010-06-22T02:59:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=filesize&rev=1277175558&do=diff filesize (reference only) filesize - return a file's size in bytes FORMAT: fsz = filesize(filename) Input fields: filename filename Output fields: fsz filesize Note: returns NaN if the file doesn't exist text/html 2010-06-21T05:23:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=flexinterpn_method&rev=1277097808&do=diff flexinterpn_method This is a proxy function for flexinterpn. It only handles some standard kernels as well as 2D to 3D data conversion for rotation. Motivation While the flexinterpn function allows very flexible interpolation of data, it would be too cumbersome to expect that every user (including myself) will create a suitable kernel window over and over again whenever data is to be interpolated. text/html 2011-05-29T02:44:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=flexinterpn&rev=1306637098&do=diff flexinterpn Note: this is a MEX (compiled) function, and it is essential for the visualization and many data processing functions of NeuroElf. Motivation When I started with writing visualization functions, I soon discovered that the interpn function of Matlab is accurate and, in some regards, much more flexible but also, to my dismay, not fast enough to handle real-time updates for when the cursor is moved in a 3-canonical-slicing view of the brain. text/html 2010-06-17T15:14:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=fmriqasheet&rev=1276787667&do=diff fmriqasheet Motivation Please refer to the information given at fmriquality. This is an auxiliary function split out of fmriquality to allow being called separately. Function reference ('help fmriqasheet') fmriqasheet - create figure with output of fmriquality FORMAT: [qs = ] fmriqasheet(q) Input fields: q return structure from fmriquality call Output fields: qs figure handle (1x1 double) text/html 2010-11-26T18:50:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=fmriquality&rev=1290797440&do=diff fmriquality Motivation As said on the quality assessment page, this function is used to determine whether or not a given dataset (run) is suitable for subsequent data analysis. Requirements To run the fMRI quality checking function, the images need to be in one of the functional imaging data formats currently supported by the xff class: text/html 2010-06-10T13:00:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=glm.removesubject&rev=1276174822&do=diff GLM::RemoveSubject - remove subject(s) from a GLM object Motivation While it is best practice to decide which subjects to include into the second level analysis before computing and creating a GLM (which then contains the selected subjects), it sometimes happens that later analyses reveal the possibility that one (or several) of the included subjects are yet outliers. text/html 2010-05-29T01:55:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=glm.rfx_rmap&rev=1275098120&do=diff GLM::RFX_rMap - simple regressions on the second level Motivation In the field of neuroscience, it is often not only of interest which areas in the brain (co- or differentially) activate for a given (set of) task(s), but also whether or not the neural correlate might be meaningful w.r.t. observed differences between subjects. text/html 2010-08-24T13:39:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=glm.singlestudy_tmap&rev=1282657168&do=diff GLM::SingleStudy_tMap Motivation After running the regression for a single study (run, i.e. one FMR, VTC, or MTC object), creating t-contrast maps for just this study can be beneficial in determining whether or not a certain run contains too much noise (or specific artefacts) for it to be included in second-level statistics. Also, it is sometimes desired to use the actually standard-error-normalized effect-statistic (t instead of regression beta) for further computations (e.g. to incorporate a… text/html 2010-06-18T23:22:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=gsr_data_analysis&rev=1276903347&do=diff GSR data analysis Motivation For many experimental tasks (e.g. subjects follwing a set of specific but differing instructions), it is often helpful to collect secondary physiological measurements, such as galvanic skin-response (GSR) over time (both as a manipulation check but also as potential candidates for mediation analysis). The recorded data often requires manual clean-up and inspection, and this page should give you some pointers as to how to conduct some of these steps. text/html 2010-06-29T17:17:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=heartbeats&rev=1277831865&do=diff heartbeats - ECG / heart-rate data analysis Motivation For many experimental tasks (e.g. subjects follwing a set of specific but differing instructions), it is often helpful to collect secondary physiological measurements, such as heart-rate over time (both as a manipulation check but also as potential candidates for mediation analysis). The data processing can be rather complicated, and a function to automatize the actual detection of heart beats in the ECG data is helpful. text/html 2011-04-14T20:21:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=importrfxglmfromspms&rev=1302812516&do=diff importrfxglmfromspms Motivation With SPM being one of the tools I found most frequently used as a neuroimaging analysis tool, NeuroElf offers a way to import an existing line of analysis (models and results of single subject, first-level regressions) into the format used by both BrainVoyager QX and NeuroElf to simplify data extraction and visualization. text/html 2010-06-23T11:43:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=map.createvmp&rev=1277293405&do=diff map.CreateVMP Motivation This method can be used to transfer a statistical map (MAP) from FMR space (where minimal smoothing is applied to the data) to the VMP format in normalized (ISO- / VTC) voxel space (and, potentially, from there to SMP format in surface space) in BrainVoyager QX. text/html 2012-10-06T15:58:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=matlab_-_datatypes&rev=1349539096&do=diff Matlab - variables, datatypes, and indexing This page covers the use of variables in Matlab, the basic (built-in) datatypes, together with some information on how they can be used, how they can be converted, and how they relate to one another. The last part covers the different indexing syntax mechanisms and some pitfalls. text/html 2012-11-12T17:45:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=matlab_-_help&rev=1352742308&do=diff Matlab - help Given the great range of functions that are already built into Matlab as well as the fact that additional functions can be added to the environment by means of “toolboxes” (folders containing sets of functions that depend on one another and that, as a whole, can be considered a program or functionality set of its own), Matlab offers a rudimentary but extremely helpful way for the user to inquire about available functions. text/html 2012-11-12T16:52:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=matlab_-_introduction&rev=1352739170&do=diff Matlab - introduction Given that NeuroElf is a Matlab toolbox with several features only available via the command line (at present at least), I want to give a short overview of Matlab, its features and how the user may be able to make better use of the available functionality. text/html 2012-11-12T22:02:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=matlab_-_language&rev=1352757745&do=diff Matlab - language elements As with any programming (or for-conversation) language, Matlab's core language has a few different types of elements that are worth understanding, as this will make it easier to read and write code that works and is robust as well as easy to understand and edit by others. text/html 2010-06-22T02:46:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=matlab_debugging&rev=1277174768&do=diff Matlab debugging This page gives a quick introduction into how to locate errors in Matlab functions (including those of the NeuroElf toolbox, I never claimed the toolbox is 100 per cent error free 8-) !) Motivation While reviewing and testing code is part of the development and implementation process, it still is a common phenomenon that some part of the code that used inside a function or batch file creates an error (usually aborting the current computation and returning to the Matlab prompt… text/html 2011-04-03T01:21:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=mdm.computeglm&rev=1301793716&do=diff MDM::ComputeGLM - compute a random-effects suitable GLM (regression) Motivation To combine several subjects' data into one compound analysis, it is custom to compute random-effects statistics on the second level. The MDM file format of BrainVoyager QX references the required time-course files (VTC or MTC) and the respective information containing the model (onsets in text/html 2011-03-15T02:44:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=mdm.voicondaverage&rev=1300157052&do=diff MDM::VOICondAverage - extract and average VOI time courses for conditions Motivation Just as statistical maps are useful to visualize whole-brain patterns of activity, it can be useful to inspect and visualize the time course properties of conditions in specific regions of the brain. text/html 2012-02-28T16:17:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=mkda&rev=1330445824&do=diff Multi-level Kernel Density Analysis (MKDA) The term Multi-level Kernel Density Analysis (MKDA) was coined by Tor Wager, and his own implementation is available at his lab's website for download. In short, the general idea is to perform the following steps * literature review and selection of articles that report spatial locations (coordinate tables) of a common neuropsychological function (or set of functions) text/html 2010-11-24T05:27:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=mtc.applyssm&rev=1290576420&do=diff MTC::ApplySSM - re-sample an MTC with a sphere-to-sphere-mapping object Motivation BrainVoyager's GLM format requires that, across subjects, the regression outputs of multiple sessions must match in the number of vertices. Given that each subject's brain reconstruction (white/gray matter boundary segmentation result) yields meshes with different numbers of vertices, and that the spatial location requires matching, the most typical approach is spherical inflation followed by a vertex-wise match… text/html 2011-04-04T20:37:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_-_all_functions&rev=1301949464&do=diff NeuroElf - all functions This page can be seen as a whole-sale reference to all function (M-) files of the toolbox. Currently, the documentation is spotty at best... Toolbox base folder, M-file list only * BVQXfile - legacy function for BVQXtools users (passes to text/html 2010-06-22T02:52:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_-_error_report&rev=1277175173&do=diff NeuroElf - reporting errors Motivation First, I would like for NeuroElf to be as error-free as possible, which then also is something other users can profit from! And while I can try as I might, I simply won't test all possible cases of application for any given function text/html 2011-05-18T13:02:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_-_surface_and_rendering_compared&rev=1305723727&do=diff NeuroElf - Surface and Rendering visualization compared text/html 2011-05-18T13:02:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_-_surface_projection_video&rev=1305723755&do=diff NeuroElf - surface projection video text/html 2011-05-18T13:04:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_basic_browsing&rev=1305723865&do=diff NeuroElf - basic browsing text/html 2014-06-18T16:26:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_changelog&rev=1403108817&do=diff NeuroElf changelog This page gives a quick overview what has changed in NeuroElf since its first publication on this website (May 17 2010) in reverse order in the following format: * date of change (first availability in a shapshot) * type of change (addition, correction, removal, etc.) and, optionally, type of object text/html 2011-05-08T02:19:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_feature_requests&rev=1304821197&do=diff NeuroElf feature requests Motivation Many (if not most) of the features being implemented in NeuroElf have been requested by colleagues. While I enjoy the process of developing algorithms and translating them into Matlab, I usually require that the product of my work is actually used. Hence I would say that if you think a feature you are missing could be of use for several labs/researchers, you are welcome to submit it for inclusion into this list (which I will update whenever a feature become… text/html 2011-04-01T22:59:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_features&rev=1301698751&do=diff NeuroElf Features While this list might not be complete, it tries to give an overview of what the NeuroElf toolbox can do (and, to some extent, what it cannot do), linking to other wiki pages containing information on how the user can achieve the required tasks with the toolbox. text/html 2011-04-03T05:25:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_compute_multi-study_glm&rev=1301808307&do=diff NeuroElf - compute multi-study GLM Motivation While looking at the outcome of regressions on single runs (e.g. via using the VTC::CreateGLM and GLM::SingleStudy_tMap methods) can already be instructive, most neuroimaging studies focus on trying to draw conclusions that can be generalized to the entirety of subject population (where the participants in the actual study represent a randomly drawn sample, and one candidate for an appropriate statistical test thus is a random-effects t-map). text/html 2011-05-18T13:03:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_contrast_manager_video&rev=1305723838&do=diff NeuroElf GUI - contrast manager (video) text/html 2011-05-18T13:19:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_contrast_manager&rev=1305724787&do=diff NeuroElf - contrast manager Motivation After performing the first-level regression of beta estimates (how much signal variation is due to the independent variables given in the design matrices, at best measured in a normalized way, e.g. after percent-signal-change transformation), it is usually required to compute random-effects statistics. text/html 2011-05-18T13:03:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_defining_rois_video&rev=1305723782&do=diff NeuroElf GUI - defining ROIs (video) text/html 2011-05-18T13:03:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_glm_beta_plotter_video&rev=1305723812&do=diff NeuroElf GUI - GLM beta plotter video text/html 2011-05-18T13:25:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_glm_beta_plotter&rev=1305725105&do=diff NeuroElf - GLM beta plotter Motivation This tool is mostly meant as a quick visualization for the assessment of whether or not a statistical test value (t-contrast) found in a specific part of the brain “makes sense” w.r.t. the hypothesis of the study, and in part also to identify outlier subjects. text/html 2014-06-04T17:46:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_global_config&rev=1401903971&do=diff NeuroElf - global configuration (variable) Motivation For the purpose of keeping a globally accessible configuration, a single 1×1 struct variable, ne_gcfg, stores settings and this wiki page describes the more important ones as a reference for scripting functionality text/html 2010-06-15T04:16:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_image_montage_ui&rev=1276575418&do=diff Image montage UI Motivation While for data inspection the screen resolution (e.g. 1mm equals one pixel for the 3-slices view) is sufficient, paper-based publication (articles, posters, etc.) usually require much higher resolution images (e.g. at least 150 dpi, which means that for those pictures, a super-sampling of at least factor 6 is required to get 25.4 * 6 = 152.4 pixels into one inch!). text/html 2011-05-12T06:30:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_keyboard_commands&rev=1305181822&do=diff NeuroElf - keyboard commands Motivation While in principle all functions can be reached via the mouse (using menu items or clicking buttons), it is sometimes “faster” (e.g. by avoiding menu items) or “more precise” (e.g. to select the current position/viewpoint) to use keyboard shortcuts. Below is a list of key bindings to function calls: text/html 2011-03-17T02:15:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_loading_data&rev=1300328155&do=diff NeuroElf - loading anatomical and functional data Motivation This is the initial step when looking at your own dataset, and thus you should try to become acquainted with NeuroElf's interface. There are several ways to load and access files from disk, which will be discussed on this page. text/html 2011-04-03T03:22:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_mdm_voi_condition_average_ui&rev=1301800975&do=diff NeuroElf - MDM VOI condition averages Motivation While hypothesis testing usually is done via formulating a Null-hypothesis (e.g. no systematic effect of differential processing of conditions), for which then a probability is given that the data could have been obtained if the Null-hypothesis were true (and a small enough p-value leading to rejection of this Null-hypothesis in favor of an alternative explanation: the difference in condition leads to a meaningful effect), false-positives can ( text/html 2011-12-08T22:28:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_menu_tree&rev=1323383292&do=diff NeuroElf - GUI menu tree Motivation This page is intended to give an overview on functions and settings available via the main menu. Each item is listed in the order of appearance and a brief explanation is given of what function is performed or how the settings are changed. text/html 2011-12-08T22:56:49+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_mkda_ui&rev=1323385009&do=diff NeuroElf - Multi-level Kernel Density Analysis (MKDA) UI Motivation When compiling a list of coordinates to be considered for an MKDA, it is often cumbersome to configure the various analyses that can be run (e.g. eliminating studies/contrasts from the analysis that do not comply with a certain methodology such as having used standardized stimuli). To overcome this relatively difficult task, NeuroElf comes with a UI that tries to simplify this as much as possible. text/html 2011-05-07T23:59:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_rendering_ui&rev=1304812775&do=diff Rendering UI Motivation Whereas slice-displays can give a very “close-to-the-data” look at results of a whole-brain mapping, it sometimes is more desirable to visualize an entire 3D space with one image. One way to do this is by using mesh-based surfaces containing a projection of statistical information. However, the extent in the third dimension (orthogonal to the surface) is not easy to visualize in (and grasp from) such images. Another look at the data is to render the entire dataset slice… text/html 2011-04-04T20:28:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_rfx_mediation&rev=1301948888&do=diff NeuroElf - RFX (single-level) mediation Motivation Contrast images assess the likelihood of observing an average brain response (across subjects) compared to its standard error under the Null-hypothesis (of no or no differential effect), and correlations assess the likelihood of observing as little residual with a predicted linear increase in those responses linked to a covariate (regressor) under the Null-hypothesis of no effect of the covariate. While this is already highly informative, it d… text/html 2011-02-28T22:59:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui_-_scripting&rev=1298933999&do=diff NeuroElf - GUI Scripting Motivation While using the GUI manually (browsing maps, setting thresholds, etc.) is usually the first step in getting a feel for the data, sometimes it is yet convenient to create a set of images (screenshots, etc.) that all have the same properties, which then becomes a matter for scripting. text/html 2011-05-18T13:23:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_gui&rev=1305725034&do=diff NeuroElf main UI Motivation While the toolbox is primarily written for advanced users who know there way around Matlab and are able to make full use of the toolbox functionality, the need for a rudimentary graphical user interface (GUI) arose soon after introducing the toolbox to my fellow lab members. text/html 2011-05-18T13:04:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_installation_video&rev=1305723882&do=diff NeuroElf Installation Video text/html 2011-08-15T14:09:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_installation&rev=1313417394&do=diff NeuroElf installation Requirements As said on the introduction page, NeuroElf requires one of the following environments: * Microsoft Windows (tested under Windows XP and Windows 7), using Matlab Version v7.5 (R2007b) and onwards * Linux (tested under S.u.S.E. Linux 11.2, 64-bit edition as well as Ubuntu 10, 32-bit edition), using Matlab Version v7.5 (R2007b) and onwards text/html 2014-06-07T04:09:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_introduction&rev=1402114177&do=diff [NeuroElf logo ] NeuroElf Introduction NeuroElf is a Matlab-based toolbox for working with neuro-imaging data. Please be aware that NeuroElf was and is not meant as a replacement for any of the more traditional and full-fledged neuro-imaging tools (such as BrainVoyager QX, SPM, AFNI, FSL, FreeSurfer, ... text/html 2014-06-07T04:14:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_license&rev=1402114482&do=diff NeuroElf license Copyright (c) 2010 - 2014, Jochen Weber All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disc… text/html 2011-04-19T02:03:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_makefiles&rev=1303178613&do=diff neuroelf_makefiles Motivation To visualize “standard space” (MNI/ICBM space) data with NeuroElf, it is often helpful to have a standardized dataset for underlay (anatomical data and surface files). Instead of bundling these files into the installation (which would require several hundreds of megabytes, even in compressed form), NeuroElf comes with functions to create these files out of a set of source files which come bundled with NeuroElf (and only require about 30 megabytes of uncompressed s… text/html 2013-02-02T00:38:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_methods&rev=1359765503&do=diff Methods implemented in NeuroElf Whenever a program is used for data analysis, it is important for the community at large to understand what algorithms were used in the analysis. And while NeuroElf is mostly written to make algorithms accessible (user friendliness aspect), it is equally relevant to ascertain that the methods implemented in any program have been accepted by the scientific community as text/html 2011-08-22T14:28:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_mex_files&rev=1314023289&do=diff NeuroElf MEX files NeuroElf comes with pre-compiled MEX files for the following platforms: * Mac OSX (10.4 and higher, PowerPC, Intel 32 and 64 bit platforms) * Windows (32 and 64 bit platforms, 64-bit version compiled with VC++ Express 2008) * text/html 2011-05-07T18:51:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_release_notes&rev=1304794267&do=diff NeuroElf release notes This page contains a per-release list of substantial additions (new features) and changes (mostly fixes) to the stable toolbox installers (or alternative flat folders) v0.9c (May 07 2011, re-release) This is a re-release adding preliminary (command-line functionality only!) compatibility with text/html 2010-05-29T22:11:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_support&rev=1275171092&do=diff NeuroElf support Given that, next to the development and maintenance of this toolbox, I have quite a few other tasks to attend to at my lab at Columbia University, direct support for the toolbox is limited. If you have a specific question, please use the following guidelines on how to get help: text/html 2011-05-18T13:10:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=neuroelf_videos&rev=1305724200&do=diff NeuroElf - Videos Here are some videos that I've recorded showing some of the more basic functionality available in NeuroElf: (for an alternative view, visit the NeuroElf YouTube Channel, which also contains playlists...) Setup Installation This video is about text/html 2010-06-12T02:26:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=obj.clearobject&rev=1276309576&do=diff obj.ClearObject Motivation As explained on the memory management page, xff stores the actual content of objects in a global variable, which means that the statement clear obj; does not have the desired effect of clearing (freeing) the memory associated with the variable (object) text/html 2010-06-12T02:37:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=obj.copyobject&rev=1276310229&do=diff obj.CopyObject Motivation While the object-oriented interface and calling convention for xff objects is suitable in most situations (e.g. a method that alters an object by, for instance, adding a volume-of-interest to a VOI file), there is the occasional need to create a temporary working copy of an object which, once the task is completed, can be discarded. Alternatively, it might be desired to create a derivate object (e.g. a VMR with a spatial filter applied) without changing the source obj… text/html 2011-04-02T23:52:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=obj.filenameondisk&rev=1301788346&do=diff obj.FilenameOnDisk Motivation This method can be used in scripted applications, for instance to store a result of a call to another method (e.g. PRT::CreateSDM) under a similar filename (see example below). Reference ('obj.Help('FilenameOnDisk')') AFT::FilenameOnDisk - returns the filename property FORMAT: filename = obj.FilenameOnDisk; No input fields Output fields: filename last used filename (on load or save) TYPES: ALL text/html 2010-06-12T19:22:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=obj.help&rev=1276370545&do=diff obj.Help Motivation This function is a means to get help on a specific method of a given object. Reference ('obj.Help('Help')') AFT::Help - method for any xff type FORMAT: [helptext] = obj.Help([methodname, onerror]); Input fields: methodname if given, only the help for one method is returned onerror checks global flag and only returns help if requested Output fields: helptext 1xN char array describing all (or one) method(s) TYPES: ALL text/html 2010-06-24T21:29:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=osz&rev=1277414967&do=diff osz (reference only) osz - returns ones(size(svzar)) FORMAT: onesws = zsz(anyvar) Input fields: anyvar any variable Output fields onesws ones with size of input argument See also zsz Notes The use of this function is deprecated (as in loops, it is faster to use text/html 2011-05-27T15:54:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=plotcurves&rev=1306511684&do=diff plotcurves Motivation Some physiological measurements require more human inspection and interaction to be good enough for additional analyses (e.g. in a GSR peak-to-peak analysis). This function allows to visualize parts of a measurement (e.g. GSR data channel) as single curves (e.g. 15-second windows following onsets). text/html 2011-08-24T17:47:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=plp.mkda&rev=1314208028&do=diff plp.MKDA Performs a multi-level kernel density analysis. Motivation Single studies can give strong evidence for a certain hypothesis (such as that a specific area of the brain is involved in processing a subset of stimuli from a greater class), but usually it is required to replicate findings for the scientific community to agree that the findings are not spurious and conclusive. Unfortunately, it is very rare that study protocols are applied in different settings (different population sample… text/html 2011-04-14T19:50:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=pmbfilter&rev=1302810628&do=diff pmbfilter (poly-mask bias filter) Motivation Depending on the sequence using for collecting structural MRI data, the output image sometimes exhibits a noticeable amount of intensity inhomogeneity bias. This is demonstrated in the screenshot below: text/html 2010-06-19T19:58:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=prefilter&rev=1276977506&do=diff prefilter The name prefilter stands for pre-processing filtering; some additional filtering might be necessary! Motivation Physiological GSR data measurements often contain quite some noise which makes analyses of those data rather difficult. This function tries to remove part of this noise by applying a derivative-based noise selection and filtering text/html 2010-05-26T23:12:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_cluster_tables&rev=1274915561&do=diff Processing stream - Cluster tables Motivation Many articles concerned with neuroimaging data exhibit one or several tables that represent each contiguous area (cluster) in the statistical map for which the values surpass the applied threshold (alpha level) and, if so configured, the size (cluster level). The following information is commonly shown: text/html 2010-06-23T20:47:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_coding_guidelines&rev=1277326073&do=diff Coding guidelines As noted on the main index page, this information is very important, particularly if you wish to collaborate with someone else on a project -- and even if not, for your own sake and soundness of your mind, do yourself the favor of taking (some of) the advice offered on this page to heart text/html 2010-10-26T19:19:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_file_formats&rev=1288120741&do=diff File formats (overview) Motivation For subsequent pages in the processing stream suggestions and instructions, it is important to be at least somewhat familiar with the various formats supported and created by NeuroElf during the course of acquiring data. This pages gives an overview and contains links to further details about each of the formats. text/html 2010-05-26T16:28:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_file_transfer&rev=1274891300&do=diff File transfer Motivation You need the files (well, it is that simple, really...) Requirements The files you wish to retrieve can be either on a fixed disk (USB key, external harddrive, CD, etc.) or, as more commonly occurring, on a machine accessible through the network. text/html 2011-04-03T02:19:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_flatmaps&rev=1301797160&do=diff Flatmaps Motivation While surface projection of results already makes a much larger amount of cortical activation visible “at a glance” (compared to showing single slices, for instance), it still requires at least two separate images for the lateral and medial portion of cortex (for one hemisphere). text/html 2010-05-30T03:36:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_image_file_conversion&rev=1275190584&do=diff Image file conversion Motivation It is very often the case that the data provided by the scanning facility is not in the format you require to perform the actual data processing and analysis. This page tries to cover the diverse format conversions that might be necessary for you to analyze your data. text/html 2011-04-03T03:47:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_preprocessing&rev=1301802444&do=diff Preprocessing Motivation Although NeuroElf is mostly meant as a tool for additional analyses that are not implemented/covered by one of the more “general-use” fMRI packages, the fact that preprocessing a whole set of subjects can easily lead to error (and is also, in part, a sometimes time-consuming task, depending on the availability of scripts), I decided to implement a text/html 2010-05-26T22:14:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_project_folder_structure&rev=1274912055&do=diff Project folder structure Motivation While you are, naturally, free to use any structure to store the diverse files related to your study (e.g. stimulus material, grant documents, physiological measurements, logfiles and onset parameters, fMRI data, structural and DTI scans, etc.), the workflow usually greatly benefits from a more rigorous adaptation and implementation of a specific folder structure. text/html 2010-10-26T19:26:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_quality_assessment&rev=1288121211&do=diff Processing stream - Quality assessment Motivation There are several things that can go wrong during the acquisition phase (scanning) of a subject, some of which severely impact the usability of a subject's dataset. While any given project (study) is still in the stage of data collection (subjects are still being scanned), there is always the chance to decide that a particular subject might introduce too much noise into the eventually performed group statistic and should be discarded (and in th… text/html 2010-06-17T19:42:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_scripted&rev=1276803773&do=diff Scripting of the processing stream (example) Motivation While for educational purposes it is quite useful to perform steps more manually, on a daily basis it is much more convenient (and less error prone) to have one or several scripts do the “work text/html 2011-05-18T13:21:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=processing_stream_-_surface_projection&rev=1305724873&do=diff Surface projection Motivation While coordinate tables allow the comparison of results between studies (given they are derived from a suitably standardized space, such as SPM's MNI space or, with some caution, TAL coordinates in BrainVoyager), it is often much easier to grasp the spatial pattern of a distributed network of activation sites if it is displayed in a three-dimensional display. text/html 2010-07-06T05:00:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=psctrans&rev=1278392419&do=diff psctrans Motivation As an alternative to z-transformation of data, applying the per cent signal change (PSC) transformation has two advantages: the signal amplitude is not altered based on variance, which means that data containing additional noise will not undergo additional scaling (unless the noise has a strong bias on the mean, that is). Additionally, data that has been PSC transformed will yield (close to) per cent signal change beta values as result of the regression equation (given that… text/html 2010-05-26T17:05:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=renamedicom&rev=1274893558&do=diff renamedicom (function reference) This function works in scripted mode, but also has its own UI window Scripting UI-based Required steps To open the UI of renamedicom, simply call the function without any arguments: renamedicom This opens the following dialog window: text/html 2010-07-06T04:39:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=root.clearobjects&rev=1278391184&do=diff root.ClearObjects This method clears several objects given by either a partial name or pattern or a simple extension. Motivation Sometimes it can happen that, during a scripted process, several orphaned objects remain in the global storage (e.g. when a multi-study design matrix is computed and an error occurs during the script). In such cases, one way to free up several objects at once is by using this method. text/html 2010-07-06T04:48:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=root.document&rev=1278391720&do=diff root.Document Motivation The reason why I wanted this method is to have an additional interface to access already loaded documents (from within scripts) without being given there handles. The method closely works together with the root.Documents method--please also read this page text/html 2010-08-04T15:44:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=root.documents&rev=1280936660&do=diff root.Documents Motivation The reason why I wanted this method is to have an additional interface to access already loaded documents (from within scripts) without being given there handles. The method closely works together with the root.Document method--please also read this page text/html 2010-08-04T16:00:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=root.help&rev=1280937655&do=diff root.Help Motivation This function is a means to get help on either a) all object types, b) a specific object type, or c) a specific method of the root object type. Reference ('root.Help('Help')') ROOT::Help - get Help on methods FORMAT: [helptext] = xff.Help([typmeth]); Input fields: typmeth optional type or method Output fields: help complete help over all methods text/html 2010-06-10T23:54:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=sdist&rev=1276214073&do=diff sdist - statistical distribution functions Motivation For many tasks in statistical hypothesis testing, it is necessary to find the ordinate value where the cumulative distibution function reaches a particular value (inverse of the CDF). These functions are available in Matlab's stats toolbox, but to allow users without this toolbox to use NeuroElf, freely available code has been edited and put into one compound function, text/html 2010-08-04T20:00:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=segmenting_brains&rev=1280952059&do=diff Segmenting brains Motivation There are several reasons why a (reasonably good) segmentation can improve the analysis and visualization of your data. For instance, BrainVoyager QX and FreeSurfer support the matching of cortical brain surface representations (meshes) to an average group mesh, which means that the localization of functional activations (cluster peaks) can be usually performed with higher precision text/html 2010-10-28T00:09:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=smp.smooth&rev=1288224561&do=diff SMP::Smooth - smooth a surface-based map Motivation For several reasons, applying additional smoothing to statistical maps can be advantageous (e.g. to compare patterns of activation across subjects and/or studies). This method allows to apply such a smoothing. text/html 2010-07-04T16:08:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=splitclustercoords&rev=1278259718&do=diff splitclustercoords Motivation Whenever clusters are reported in tables, it frequently happens that distinct areas are grouped into one cluster, e.g. due to the fact that the selected threshold simply makes them appear connected whereas there is clear a priori evidence (or even knowledge, as in cases where for instance the left and right hemispheric activations in visual cortex as text/html 2011-04-03T04:23:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=spm5_preprojobs&rev=1301804588&do=diff spm5_preprojobs Motivation As said on the page describing the UI-based configuration of SPM5/SPM8 preprocessing in NeuroElf, this function is mostly meant to ensure that all subjects are preprocessed using the same parameters (and that all steps are performed in their entirety and same order). Requirements text/html 2010-07-25T13:07:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=srf.backtovmr&rev=1280063267&do=diff srf.BackToVMR Motivation After creating/morphing a surface, it is often helpful to visualize in a voxel-based representation where the vertices (and triangular planes inbetween) are located in space. This method allows to do so by creating either a 1mm- or a 0.5mm- resolution dataset which can then be sampled (or merged with a VMR, the original purpose). text/html 2016-05-27T15:19:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=start&rev=1464362367&do=diff NeuroElf wiki [NeuroElf logo]Welcome to the NeuroElf wiki. If you would like to contribute, please read the information provided in the wiki internals section below, email register (at) neuroelf (dot) info, and once you get your user information, you can edit/add articles! :) text/html 2011-04-04T19:12:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=transio&rev=1301944335&do=diff transio (transparent file I/O access class) Motivation Neuroimaging datasets can easily reach very large sizes (e.g. running a study with 2 groups of 24 subjects each and a 3x2x2 within-subject design requires to store a total of at least 48 * 13 = 624 maps, if each of these maps fully covers the brain at a 3mm resolution this amounts to up to 200,000 voxels per map requiring 800,000 bytes of diskspace leading to a total of about 500MByte of required storage capacity). text/html 2010-06-22T03:22:29+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=uint322colcode&rev=1277176949&do=diff uint322colcode (reference only) uint322colcode - convert from uint32 to colcode array FORMAT: outarray = uint322colcode(inarray) Input fields: inarray Nx1 (or 1xN) input array of type uint32 Output fields: outarray Nx4 double array (n, 1) = color index or NaN (n, 2) = red component (0...255) (n, 3) = green component (0...255) (n, 4) = blue component (0...255) See a… text/html 2010-05-26T20:45:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=uploading_image_files&rev=1274906734&do=diff Uploading image files Motivation Images often have the ability to convey information (either by themselves or in combination with text, e.g. as to explain where to click in a specific dialog) much better than written information alone. It is thus important to augment articles where necessary with a form of visualization. text/html 2014-06-04T17:57:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=vmp.clustertable&rev=1401904636&do=diff obj.ClusterTable Motivation As part of the analysis output for a whole-brain search (i.e. next to images of whole-brain statistical maps for instance), people usually include tables of activation peaks into their manuscripts. This method allows to create such tables with the following features: text/html 2010-10-09T14:17:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=vmp.computeformula&rev=1286633858&do=diff vmp.ComputeFormula Motivation It is often helpful to combine the maps from a VMP in various ways (e.g. to create a conjunction map). This method allows various combination options. Method reference ('vmp.Help('ComputeFormula')') VMP::ComputeFormula - add a conjunction map to a VMP FORMAT: [vmp] = vmp.ComputeFormula(formula [, opts]) Input fields: formula string giving a formula, supporting the following #i -> .Map(i).VMPData $i… text/html 2010-06-14T19:00:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=vmp.createsmp&rev=1276542041&do=diff vmp.CreateSMP Motivation Please refer to the Surface projection page for information on why to use this method and a practical example output. Method reference ('vmp.Help('CreateSMP')') VMP::CreateSMP - sample SMPs from the maps in a VMP FORMAT: smp = vmp.CreateSMP(srf, opts) Input fields: srf required surface file opts 1x1 struct with optional fields .interp method ('nearest', {'linear'}, 'cubic') .ipfrom interpolate from P … text/html 2010-06-22T19:32:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=vmr.applytrf&rev=1277235138&do=diff vmr.ApplyTRF Motivation The main motivation for using this function is the ability to flexibly script spatial VMR transformation in Matlab. Method reference ('vmr.Help('ApplyTRF')') VMR::ApplyTRF - apply transformation to VMR FORMAT: newvmr = vmr.ApplyTRF(trf [, opts]) Input fields: trf TRF object opts struct with optional fields .asdouble store output as double (default: false) .inverse apply inverse transformation (default: fa… text/html 2010-08-11T13:35:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=vmr.createvtc&rev=1281533718&do=diff vmr.CreateVTC Motivation The main motivation for using this function is the ability to flexibly script VTC creation from FMR files using transformation files created in BrainVoyager QX (coregistration initial and fine alignment, as well as ACPC and TAL normalization files). text/html 2011-04-14T20:54:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=vmr.inhomogeneitycorrect&rev=1302814450&do=diff VMR::InhomogeneityCorrect - perform inhomogeneity correction Motivation For an overview of the topic, please refer to the pmbfilter page (this function is used as part of this method). Method reference ('vmr.Help('InhomogeneityCorrect')') VMR::InhomogeneityCorrect - attempt automatic inhomogeneity correction FORMAT: [vmr = ] vmr.InhomogeneityCorrect([opts]) Input fields: opts optional struct with settings .mask either 3D uint8/logical data or VMR ob… text/html 2010-06-22T19:58:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=vmrspmcoreg&rev=1277236727&do=diff vmrspmcoreg Motivation The main motivation for this function is to cross-check BrainVoyager's registration quality with that of SPM (once again cross-checked with manual inspection, of course). Requirements For this function to work, either SPM5 or SPM8 must be available on the path. For SPM8, it is important that all required subfolders (e.g. matlabbatch, etc.) are already on the path. If in doubt, use text/html 2010-06-28T19:07:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=voi.addsphericalvoi&rev=1277752020&do=diff voi.AddSphericalVOI Motivation In many cases, researchers already have a priori selected areas/regions which are candidates for testing specific hypothesis, which gives greater detection power (at least when, on the other hand, researchers apply customary multiple-comparison correction algorithm if they decide to perform whole-brain searches for effects that match their hypothesis!). text/html 2011-04-15T19:09:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=working_with_statistics&rev=1302894563&do=diff Working with statistics Motivation While a single statistical map is already informative, often it is necessary to combine the information of two (or several) different analyses together (e.g. by applying a mask or restricting the statistic by the minimum value across two or more maps) to come to more reliable evidence for an effect. text/html 2011-03-31T18:07:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xff_-_file_formats&rev=1301594859&do=diff xff file formats Motivation Sometimes it is useful to understand the working mechanism of a specific file format supported by NeuroElf/xff, particularly for the text-based (tff) formats (e.g. BrainVoyager QX's protocol file format). This page will, in time, link to information about the various formats. text/html 2010-06-24T14:46:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xff_-_map_format&rev=1277390815&do=diff MAP (BrainVoyager QX's FMR-based map) file format Motivation The more common case of running statistics is in either 3D voxel (VTC/VMP) space, but there are still quite a few applications for running statistics with data that has been altered as little as possible (minimal preprocessing). The MAP format provides the ability to store a slice-based maps that match the FMR layout. At this point, there is no support for storing multiple statistics per FMR voxel. text/html 2010-06-29T17:28:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xff_-_mat_format&rev=1277832516&do=diff MAT (Matlab MAT file with data field) Motivation The file formats that support reading channel recordings (ACQ and NTT) cannot be saved back to disk. It was a choice of convenience to create a (more or less) compatible format that can be easily saved (and also is available later without the toolbox). text/html 2011-03-31T18:02:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xff_-_mdm_format&rev=1301594555&do=diff MDM (BrainVoyager QX's Multiple-Design-Matrix) file format Motivation For several reasons, it is useful to be able to inspect and alter the list of studies used in particular analysis (e.g. to use a search-and-replace edit command in case files have been moved). text/html 2010-06-10T13:34:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xff_-_memory_management&rev=1276176885&do=diff xff - memory management Motivation Matlab's only way of passing arguments into a called function is “by-value”, which means that if the called function alters a variable (which can be highly complex, such as a nested struct!), the calling function needs to accept any such altered variables as returned values and re-assign them to their original variables. Here is an example: text/html 2010-06-16T17:20:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xff_-_prt_format&rev=1276708823&do=diff PRT (BrainVoyager QX's Protocol) file format Motivation For several reasons, it is useful to be able to inspect and alter the experimental design in a human-readable form (text). General setup The information contained in BrainVoyager QX text files is either given in the form: text/html 2010-06-12T01:46:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xff_-_sdm_format&rev=1276307208&do=diff SDM (BrainVoyager QX's Single-study design matrix) file format Motivation The most common approach to identify brain areas that are active during a specific task is by creating regressors used in a multiple linear regression model (General Linear Model; GLM). BrainVoyager QX uses a text-based file format that, after applying a convolution to the stimulus-based stick- or block functions, stores a set of columns, each representing one of the experimental conditions (or parametric modulations of … text/html 2011-04-04T17:43:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xff_-_vtc_format&rev=1301938996&do=diff VTC (BrainVoyager QX's volume-based time-course) file format Motivation Most neuroimaging programs store functional data as a series of 3D volumes (separate files) or as a four-dimensional array, where still time is the slowest increasing index (in Matlab this refers to the last index). While this makes it convenient to display one of the volumes out of a time series, it usually makes regressing or plotting (averaged) timecourses a little more computational. text/html 2011-03-31T21:01:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xff&rev=1301605260&do=diff xff (class for file IO) Motivation Neuroimaging data comes in various formats, among of the more prominent ones are * Analyze/NIftI (e.g. used in the SPM series) * DICOM (a format that several scanners use to store/transport imaging data) * PAR/REC (a Philips proprietary, text and binary compound file format) text/html 2011-04-04T18:27:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xfigure&rev=1301941627&do=diff xfigure (class for UI object handling) Motivation When I started writing Matlab code for handling UI events (using Matlab R11), I noticed that certain tasks were not at all easy to accomplish and that using the built-in figure editor was a bit cumbersome (for me, at least). I thus decided to come up with a set of functions that would manipulate Matlab's handle graphics objects (particularly figures and uicontrols), which ended up becoming a class implementation, xfigure. text/html 2011-04-04T20:00:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=xini&rev=1301947212&do=diff xini (ini/configuration file handling class) Motivation Storing configuration settings in .MAT-files makes it sometimes more cumbersome to change those settings (particularly when trying to compare a prior set to the currently used one). In such cases, it can be helpful to store the settings in a text file. text/html 2010-06-24T21:28:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=zsz&rev=1277414923&do=diff zsz (reference only) zsz - returns zeros(size(svzar)) FORMAT: zerosws = zsz(anyvar) Input fields: anyvar any variable Output fields zerosws zeros with size of input argument See also osz Notes text/html 2010-06-11T00:04:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://neuroelf.com/wiki/doku.php?id=ztrans&rev=1276214685&do=diff ztrans Motivation Under certain circumstances (e.g. data that is arbitrarily scaled and comes from several sources has to be compared), one way to normalize (re-scale) the data is to apply z-transformation (setting the mean of values in the desired dimension to 0 and the standard deviation to 1).