documentation / faq /
Frequently asked questions
On this page you can find answers to a variety of FieldTrip and MATLAB related questions.
We invite you to add your own tutorials to the website, considering the documentation guidelines. Whenever you explain somebody in person or over email how to do something with FieldTrip, please consider whether you could use the website for this, allowing others to learn from it as well.
See also the tutorials and example scripts.
Reading and preprocessing data
Specific data formats
- How can I deal with a discontinuous Neuralynx LFP recording?
- How can I extend the reading functions with a new dataformat?
- How can I fix a corrupt CTF meg4 file?
- How can I fix a corrupt CTF res4 header file?
- How can I import my own data format?
- How can I inspect the electrode impedances of my BrainVision data?
- How can I read all channels from an EDF file that contains multiple sampling rates?
- How can I read corrupted (unsaved) CTF data?
- How can I read EGI mff data without the JVM?
- How does the CTF higher-order gradiometer work?
- I am having problems reading the CTF .hc headcoordinates file
- I have problems reading in NeuroScan .cnt files. How can I fix this?
- Why are the fileio functions stateless, does the fseek not make them very slow?
- Why should I set continuous to yes for CTF data?
- Why should I start with rereferencing for BioSemi EEG data?
Data handling
- How can I append the files of two separate recordings?
- How can I convert one dataformat into an other?
- How can I merge two datasets that were acquired simultaneously with different amplifiers?
- How can I preprocess a dataset that is too large to fit into memory?
- How can I rename channels in my data structure?
- Reading is slow, can I write my raw data to a more efficient file format?
- What dataformats are supported?
Trials, triggers and events
- How can I check or decipher the sequence of triggers in my data?
- How can I find out what eventvalues and eventtypes there are in my data?
- How can I process continuous data without triggers?
- How can I transform trigger values from bits to decimal representation with a trialfun?
- Is it possible to keep track of trial-specific information in my analysis pipeline?
- What is the relation between "events" (such as triggers) and "trials"?
Artifacts
- Do I need to resample my data, and if so, how is this to be done?
- How can I consistently represent artifacts in my data?
- How can I interpret the different types of padding in FieldTrip?
- How does the filter padding in preprocessing work?
- I used ICA on my MEG data from before 2012 and now FieldTrip crashes, why is that?
- Should I rereference prior to or after ICA for artifact removal?
- What kind of filters can I apply to my data?
- Why does my ICA eyeblink component look strange?
- Why does my ICA output contain complex numbers?
- Why is there a residual 50Hz line-noise component after applying a DFT filter?
Spectral analysis
- Does it make sense to subtract the ERP prior to time frequency analysis, to distinguish evoked from induced power?
- How can I compute inter-trial coherence?
- How can I do time-frequency analysis on continuous data?
- How does mtmconvol work?
- How to interpret the sign of the phase slope index?
- In what way can frequency domain data be represented in FieldTrip?
- What convention is used to define absolute phase in 'mtmconvol', 'wavelet' and 'mtmfft'?
- What does "padding not sufficient for requested frequency resolution" mean?
- What is meant by time-frequency trade off?
- What is the difference between coherence and coherency?
- Why am I not getting integer frequencies?
- Why does my output.freq not match my cfg.foi when using 'mtmconvol' in ft_freqanalysis?
- Why does my output.freq not match my cfg.foi when using 'mtmfft' in ft_freqanalysis
- Why does my output.freq not match my cfg.foi when using 'wavelet' (formerly 'wltconvol') in ft_freqanalysis?
- Why does my TFR contain NaNs?
- Why does my TFR look strange (part I, demeaning)?
- Why does my TFR look strange (part II, detrending)?
- Why is the largest peak in the spectrum at the frequency which is 1/segment length?
Source reconstruction
- Can I do combined EEG and MEG source reconstruction?
- Can I restrict the source reconstruction to the grey matter?
- How are electrodes, magnetometers or gradiometers described?
- How are the different head and MRI coordinate systems defined?
- How are the Left and Right Pre-Auricular (LPA and RPA) points defined?
- How can I check whether the grid that I have is aligned to the segmented volume and to the sensor gradiometer?
- How can I convert an anatomical MRI from DICOM into CTF format?
- How can I determine the anatomical label of a source or electrode?
- How can I fine-tune my BEM volume conduction model?
- How can I map source locations onto an anatomical label in an atlas?
- How can I visualize the different geometrical objects that are needed for forward and inverse computations?
- How do homogenous coordinate transformation matrices work?
- How do I install the OpenMEEG binaries
- How is a segmentation defined?
- How is anatomical, functional or statistical "volume data" described?
- How should I report the positions of the fiducial points on the head?
- How should I specify the fiducials for electrode realignment?
- How to change the MRI orientation, the voxel size or the field-of-view?
- How to coregister an anatomical MRI with the gradiometer or electrode positions?
- Is it good or bad to have dipole locations outside of the brain for which the source reconstruction is computed?
- Is it important to have accurate measurements of electrode locations for EEG source reconstruction?
- Is it OK for vertices/dipoles to stick out of the volume conductor?
- My MRI is upside down, is this a problem?
- Should I use a Polhemus or a Structure Sensor to record electrode positions?
- What is the conductivity of the brain, CSF, skull and skin tissue?
- What is the difference between the ACPC, MNI, SPM and TAL coordinate systems?
- What kind of volume conduction models of the head (head models) are implemented?
- What material is used for the flexible MEG headcasts?
- Where can I find the dipoli command-line executable?
- Where is the anterior commissure?
- Why does my EEG headmodel look funny?
- Why is the source model deformed or incorrectly aligned after warping template?
- Why is there a rim around the brain for which the source reconstruction is not computed?
- Why should I use an average reference for EEG source reconstruction?
Statistical analysis
- How can I define neighbouring sensors?
- How can I determine the onset of an effect?
- How can I test an interaction effect using cluster-based permutation tests?
- How can I test for correlations between neuronal data and quantitative stimulus and behavioral variables?
- How can I test whether a behavioral measure is phasic?
- How can I use the ivar, uvar, wvar and cvar options to precisely control the permutations?
- How does a difference in trial numbers per condition affect my statistical test
- How does ft_prepare_neighbours work?
- How NOT to interpret results from a cluster-based permutation test
- Should I use t or F values for cluster-based permutation tests?
- What is the idea behind statistical inference at the second-level?
- Why are there multiple neighbour templates for the Neuromag306 system?
- Why should I use the cfg.correcttail option when using statistics_montecarlo?
Plotting and visualization
- How can I play back EEG/MEG and synchronous audio or video?
- How can I use the databrowser?
- How can I visualize a localspheres volume conductor model?
- How do I construct a layout file for the plotting functions?
- I am getting strange artifacts in figures that use opacity
- I am having problems printing figures that use opacity
- What are the different Neuromag/Elekta/Megin and Yokogawa layouts good for?
- What is a good way to save images for later processing in other software?
- What is the format of the layout file which is used for plotting?
- What is the plotting convention for anatomical MRIs?
- Which colormaps are supported?
- Why does my anatomical MRI show upside-down when plotting it with ft_sourceplot?
Experimental questions
- How can I change the head localization in a CTF dataset?
- How can I monitor a subject's head position during a MEG session?
- How can I use my MacBook Pro for stimulus presentation in the MEG lab?
- How can I visualize the Neuromag head position indicator coils?
- What kind of cable do I need for a serial port connection between two computers?
Realtime data streaming and analysis
- Does the FieldTrip realtime buffer only work with MATLAB?
- How fast is the FieldTrip buffer for realtime data streaming?
- How should I get started with the FieldTrip realtime buffer?
Distributed computing
- What are the different approaches I can take for distributed computing?
- How to get started with distributed computing using qsub?
- How to get started with the MATLAB distributed computing toolbox?
- How to compile MATLAB code into stand-alone executables?
MATLAB questions
- Can I prevent "external" toolboxes from being added to my MATLAB path?
- Can I use FieldTrip without MATLAB license?
- Can I use Octave instead of MATLAB?
- How can I compile the mex files and command-line executables?
- How can I compile the mex files on 64-bit Windows?
- How can I compile the mex files on macOS?
- How many lines of code does FieldTrip consist of?
- How to select the correct SPM toolbox?
- Installation and setting up the path
- MATLAB complains about a missing or invalid mex file, what should I do?
- MATLAB complains that mexmaci64 cannot be opened because the developer cannot be verified
- MATLAB does not see the functions in the "private" directory
- MATLAB version 7.3 (2006b) crashes when I try to do ...
- Replacements for functions from MathWorks toolboxes
- The databrowser crashes and destroys the whole MATLAB session, how can I resolve this?
- What are the MATLAB and external requirements?
- What are the MATLAB requirements for using FieldTrip?
- Which external toolboxes are used by FieldTrip?
- Why are so many of the interesting functions in the private directories?
Code and development questions
- How are the various MATLAB data structures defined?
- How can I debug my analysis script if a FieldTrip function gives an error?
- How can I keep track of changes to the code?
- What does a typical call to a FieldTrip function look like?
- Why was FieldTrip maintained in SVN and not in Git?
Organizational questions
- Can I get an offline version of the documentation on the website?
- Can I use the FieldTrip logo on my poster?
- How many people are subscribed to the email discussion list?
- How should I refer to FieldTrip in my publication?
- How should I share example data with the email list or developers?
- How to ask good questions to the community?
- I am having problems downloading
- I am working at the Donders, should I also download FieldTrip?
- Which version of FieldTrip should I download?
- Why am I not allowed to post to the discussion list?
- Why am I not receiving emails from the discussion list?
- Why am I receiving warnings about too many bouncing emails?
- Why is FieldTrip developed separately from EEGLAB?
- Why is my message rejected from the email discussion list?
Various other questions
- Are the FieldTrip lectures available on video?
- Can I compare EEG channels between different electrode caps?
- Can I organize my own FieldTrip workshop?
- How can I anonymize or deidentify a BrainVision dataset?
- How can I anonymize or deidentify a CTF dataset?
- How can I anonymize or deidentify an anatomical MRI?
- How can I anonymize or deidentify data processed in FieldTrip?
- How can I anonymize or deidentify DICOM files?
- How can I share my MEG data?
- How do I prevent FieldTrip from printing the time and memory after each function call?
- How should I prepare for the upcoming FieldTrip workshop?
- How should I specify the coordinate systems in a BIDS dataset?
- What are the units of the data and of the derived results?
- Where can I find open access MEG/EEG data?
- Where can I find open hardware for MEG and EEG?
- Which datasets are used in the documentation and where are they used?
- Which methodological details should I report in an EEG/MEG manuscript?
- Which version of FieldTrip should I download?