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TYPO - as identified from the ignore wordlist (#703)
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* TYPO - as identified from the ignore wordlist, after a lenient first pass by a human reader
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2 changes: 1 addition & 1 deletion _includes/shared/faq/external.md
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Expand Up @@ -27,7 +27,7 @@ A number of external toolboxes is included in the `fieldtrip/external` subdirect
- egi_mff_v2
- ezc3d
- [fastica](http://research.ics.tkk.fi/ica/fastica/) for independent component analysis
- [fileexchange](https://www.mathworks.com/matlabcentral/fileexchange) varous functions from Mathworks File Exchange
- [fileexchange](https://www.mathworks.com/matlabcentral/fileexchange) various functions from Mathworks File Exchange
- fns
- freesurfer to read MRI data
- gcmi
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Expand Up @@ -26,7 +26,7 @@ The two UO-types (**subjects** and **trials**) and the two experimental designs

The statistical testing in FieldTrip is performed by the functions **[ft_timelockstatistics](/reference/ft_timelockstatistics)** and **[ft_freqstatistics](/reference/ft_freqstatistics)**. From a statistical point of view, the calculations performed by these two functions are very similar. These functions differ with respect to the data structures on which they operate: **[ft_timelockstatistics](/reference/ft_timelockstatistics)** operates on data structures produced by **[ft_timelockanalysis](/reference/ft_timelockanalysis)** and **[ft_timelockgrandaverage](/reference/ft_timelockgrandaverage)**, and **[ft_freqstatistics](/reference/ft_freqstatistics)** operates on data structures produced by **[ft_freqanalysis](/reference/ft_freqanalysis)**, **[ft_freqgrandaverage](/reference/ft_freqgrandaverage)**, and **[ft_freqdescriptives](/reference/ft_freqdescriptives)**.

To correct for multiple comparisons, one has to specify the field cfg.correctm. This field can have the values 'no', 'max', 'cluster', 'bonferoni', 'holms', or 'fdr'. In this tutorial, we only use cfg.correctm = 'cluster', which solves the MCP by calculating a so-called cluster-based test statistic and its significance probability.
To correct for multiple comparisons, one has to specify the field cfg.correctm. This field can have the values 'no', 'max', 'cluster', 'bonferroni', 'holms', or 'fdr'. In this tutorial, we only use cfg.correctm = 'cluster', which solves the MCP by calculating a so-called cluster-based test statistic and its significance probability.

#### The calculation of this cluster-based test statistic

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Expand Up @@ -103,7 +103,7 @@ From the autoregressive coefficients it is now possible to compute the spectral
dof: 500
label: {3x1 cell}
dimord: 'chan_chan_freq'
cfg: [1x1 struct]
cfg: [1x1 struct]

The resulting **mfreq** data structure contains the pairwise transfer function between the 3 channels for 101 frequencies.

Expand Down Expand Up @@ -132,7 +132,7 @@ Some connectivity metrics can be computed from a non-parametric spectral estimat
The resulting **freq** structure contains the spectral estimate for 3 tapers in each of the 500 trials (hence 1500 estimates), for each of the 3 channels and for 101 frequencies. It is not necessary to compute the cross-spectral density at this stage, because the function used in the next step, **[ft_connectivityanalysis](/reference/ft_connectivityanalysis)**, contains functionality to compute the cross-spectral density from the Fourier coefficients.

{% include markup/warning %}
We apply frequency smoothing of 2Hz. The tapsmofrq parameter should already be familiar to you from the [multitapers section of the frequency analysis tutorial](/tutorial/timefrequencyanalysis/#multitapers). How much smoothing is desired will depend on your research question (i.e. frequency band of interest) but also on wether you decide to use the parametric or non-parametric estimation methods for connectivity analysis:
We apply frequency smoothing of 2Hz. The tapsmofrq parameter should already be familiar to you from the [multitapers section of the frequency analysis tutorial](/tutorial/timefrequencyanalysis/#multitapers). How much smoothing is desired will depend on your research question (i.e. frequency band of interest) but also on whether you decide to use the parametric or non-parametric estimation methods for connectivity analysis:

Parametric and non-parametric estimation of Granger causality yield very comparable results, particularly in well-behaved simulated data. The main advantage in calculating Granger causality using the non-parametric technique is that it does not require the determination of the model order for the autoregressive model. When relying on the non-parametric factorization approach more data is required as well as some smoothing for the algorithm to converge to a stable result. Thus the choice of parametric vs. non-paramteric estimation of Granger causality will depend on your data and your certainty of model order.
(find this information and more in [Bastos and Schoffelen 2016](http://journal.frontiersin.org/article/10.3389/fnsys.2015.00175/full))
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4 changes: 2 additions & 2 deletions _includes/shared/tutorial/headmodel_read_align.md
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Expand Up @@ -24,7 +24,7 @@ The structure of the `mri` variable contains the following fields:

- `dim` gives information on the size (i.e. the number of voxels) of the anatomical volume into each direction
- `anatomy` is a matrix (with the size and number of dimensions specified in `dim`) that contains the anatomical information
- `hdr` contains the detailled header information from the original file, it contents vary, depending on the file format
- `hdr` contains the detailed header information from the original file, it contents vary, depending on the file format
- `transform` is a homogenous [transformation matrix](/faq/homogenous) that allows expressing the voxel positions (in the field `anatomy`) in a certain coordinate system
- `fid` is an optional structure with fiducial information, this will in general not be present
- `coordsys` specifies the coordinate system
Expand Down Expand Up @@ -92,4 +92,4 @@ If we did not pay attention to the anatomical landmarks when looking at **[ft_so
cfg.coordsys = 'ctf'; % the desired coordinate system
mri_realigned = ft_volumerealign(cfg, mri)

Identifying the nasion is easy. However, it is difficult, if not impossible, to visually distinguish the left and right side from the anatomical MRI. That is why at the DCCN (where this scan was made) we _always_ include a vitamine-E capsule at the right side of the head. Sometimes teh vitamine-E capsule is taped on the right mastoid, sometimes it is taped into the right earshell of the protective headphones. To determine the rpa in this specific MRI, you first search for the vitamine-E capsule and then search for the fiducial that marks the right ear canal. Once the rpa been determined, you can move on to the lpa. Other labs might use vitamine-E capsules at the anatomical landmarks themselves, or might not use any fiducials, so please update your own coregistration procedure accordingly.
Identifying the nasion is easy. However, it is difficult, if not impossible, to visually distinguish the left and right side from the anatomical MRI. That is why at the DCCN (where this scan was made) we _always_ include a vitamine-E capsule at the right side of the head. Sometimes the vitamine-E capsule is taped on the right mastoid, sometimes it is taped into the right earshell of the protective headphones. To determine the rpa in this specific MRI, you first search for the vitamine-E capsule and then search for the fiducial that marks the right ear canal. Once the rpa been determined, you can move on to the lpa. Other labs might use vitamine-E capsules at the anatomical landmarks themselves, or might not use any fiducials, so please update your own coregistration procedure accordingly.
2 changes: 1 addition & 1 deletion _posts/2020-05-28-reference-docs-on-github.md
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Expand Up @@ -5,7 +5,7 @@ categories: [news]

### 28 May, 2020

We have changed the links to the reference documentation (i.e. the help that is at the start of each FieldTrip function) here on the website such that they now point to the code on GitHub, rather than to a Markdown copy of the fucntion help on the website. This makes it possible to scroll down past the help, and to look at the code and the details of the implementation. Also, it makes it easier for you to contribute your suggestions to the help or to the code itself: You can simply click on the "pencil" symbol in the upper right corner.
We have changed the links to the reference documentation (i.e. the help that is at the start of each FieldTrip function) here on the website such that they now point to the code on GitHub, rather than to a Markdown copy of the function help on the website. This makes it possible to scroll down past the help, and to look at the code and the details of the implementation. Also, it makes it easier for you to contribute your suggestions to the help or to the code itself: You can simply click on the "pencil" symbol in the upper right corner.

{% include image src="/assets/img/posts/github_edit.png" width="291" %}

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2 changes: 1 addition & 1 deletion _posts/2020-06-11-improved-colormap-handling.md
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Expand Up @@ -7,4 +7,4 @@ categories: [news]

Robert and Jan-Mathijs have made an improvement to how color schemes can be specified. In functions supporting cfg.colormap, you can now also specify a subset of the color schemes that are in matplotlib, as well as the brewermap color schemes (e.g., 'RdBu'). See **[ft_colormap](/reference/plotting/ft_colormap)** for more information.

In this [movie](https://youtu.be/IEGPslJoIE0) you can see Robert and Jan-Mathijs working on this. And finally, as a bonus, we have added an 'ftcolors' colormap, which will give your artwork this extra FieldTrippy feel. Happy plotting!
In this [movie](https://youtu.be/IEGPslJoIE0) you can see Robert and Jan-Mathijs working on this. And finally, as a bonus, we have added an 'ftcolors' colormap, which will give your artwork this extra FieldTrip like feel. Happy plotting!
2 changes: 1 addition & 1 deletion _posts/2020-06-24-bug-in-precomputed-leadfields.md
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Expand Up @@ -9,6 +9,6 @@ We are sorry to report that with merging the recent pull request [#1377](https:/

Specifically, the handling of the defaults for `cfg.reducerank` and the `cfg.backproject` changed a bit, which had an unforeseen sideeffect in `ft_prepare_leadfield`, **if** (and only if) you used this function for the computation of MEG-based leadfields, using the `singleshell` method. Specifically, `ft_prepare_leadfield` would by default compute MEG singleshell leadfields with `reducerank=2` (this is how it always has been), but it would wrongly backproject (i.e. the intended projection of the rank-reduced 2-column leadfield back into 3D space with a column for the x, y, and z dipole moment in Cartesian space) the rank-reduced leadfield. Rather, `ft_prepare_leadfield` would on [line 292](https://github.com/fieldtrip/fieldtrip/blob/af5f9822413d11e66f3821943e945e98ab766da6/ft_prepare_leadfield.m#L292) discard the last column. The error was due to MATLAB interpreting `if []` as false, causing on line 295 only the first two columns to be copied to the output. Consequently, the leadfield for the z-direction was discarded.

Are you affected? If you used the master branch from GitHub (which is the development version), or a release version between **20200529** and **20200607**, and if you have used `ft_prepare_leadfield` for MEG with singleshell models, then you are likely affected. You can check yourself: your precomputed leadfields should have three columns; if they only have two columns and you did not explicityly specify `reducerank` and `backproject` in your configuration, your leadfields are wrong. Other models than MEG singleshell are not affected.
Are you affected? If you used the master branch from GitHub (which is the development version), or a release version between **20200529** and **20200607**, and if you have used `ft_prepare_leadfield` for MEG with singleshell models, then you are likely affected. You can check yourself: your precomputed leadfields should have three columns; if they only have two columns and you did not explicitly specify `reducerank` and `backproject` in your configuration, your leadfields are wrong. Other models than MEG singleshell are not affected.

To resolve the problem, please update to the latest **20200623** release version from the [download server](https://download.fieldtriptoolbox.org/) or from the [GitHub release page](https://github.com/fieldtrip/fieldtrip/releases) and recompute your leadfields, source estimates, etcetera.
2 changes: 1 addition & 1 deletion _posts/2020-08-20-release.md
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Expand Up @@ -7,7 +7,7 @@ tweet: FieldTrip version 20200820 was just released. See http://www.fieldtriptoo
### 20 August, 2020

FieldTrip version [20200820](http://github.com/fieldtrip/fieldtrip/releases/tag/20200820) has been released.
See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20200820...20200821) for the detailled list of updates.
See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20200820...20200821) for the detailed list of updates.

#### Commits

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2 changes: 1 addition & 1 deletion _posts/2020-09-11-release.md
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Expand Up @@ -6,4 +6,4 @@ tweet: FieldTrip version 20200911 was just released, now with support for SNIRF

### 11 September, 2020

FieldTrip version [20200911](http://github.com/fieldtrip/fieldtrip/releases/tag/20200911) has been released. This includes improvements for reading and writing SNIRF data, converting data in Homer format and other improvements for NIRS data. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20200831...20200911) for the detailled list of updates. See also [getting started with NIRS](/getting_started/#getting-started-with-nirs-data) for updated documentation.
FieldTrip version [20200911](http://github.com/fieldtrip/fieldtrip/releases/tag/20200911) has been released. This includes improvements for reading and writing SNIRF data, converting data in Homer format and other improvements for NIRS data. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20200831...20200911) for the detailed list of updates. See also [getting started with NIRS](/getting_started/#getting-started-with-nirs-data) for updated documentation.
2 changes: 1 addition & 1 deletion _posts/2020-10-09-release.md
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Expand Up @@ -6,4 +6,4 @@ tweet: FieldTrip version 20201009 was just released with improved NIRS reading t

### 09 October, 2020

FieldTrip version [20201009](http://github.com/fieldtrip/fieldtrip/releases/tag/20201009) has been released with various improvements and bug fixes, including improved NIRS reading thanks to Janny Stapel. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20200919...20201009) for the detailled list of updates.
FieldTrip version [20201009](http://github.com/fieldtrip/fieldtrip/releases/tag/20201009) has been released with various improvements and bug fixes, including improved NIRS reading thanks to Janny Stapel. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20200919...20201009) for the detailed list of updates.
2 changes: 1 addition & 1 deletion _posts/2021-01-28-release.md
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Expand Up @@ -6,4 +6,4 @@ tweet: FieldTrip version 20210128 was just released with several fixes to our st

### 28 January, 2021

FieldTrip version [20210128](http://github.com/fieldtrip/fieldtrip/releases/tag/20210128) has been released. This verion contrains updates to **[ft_statistics_montecarlo](/reference/ft_statistics_montecarlo)**, **[ft_connectivityanalysis](/reference/ft_connectivityanalysis)** and source modelling using **eLORETA**. Brought to you by [Tibor Auer](https://github.com/tiborauer) and JM! See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20210121...20210128) for the detailed list of updates.
FieldTrip version [20210128](http://github.com/fieldtrip/fieldtrip/releases/tag/20210128) has been released. This version constrains updates to **[ft_statistics_montecarlo](/reference/ft_statistics_montecarlo)**, **[ft_connectivityanalysis](/reference/ft_connectivityanalysis)** and source modelling using **eLORETA**. Brought to you by [Tibor Auer](https://github.com/tiborauer) and JM! See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20210121...20210128) for the detailed list of updates.
2 changes: 1 addition & 1 deletion _posts/2021-02-12-release.md
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Expand Up @@ -6,4 +6,4 @@ tweet: FieldTrip 20210212 was just released with FEM for EEG and MEG based on ht

### 12 February, 2021

FieldTrip version [20210212](http://github.com/fieldtrip/fieldtrip/releases/tag/20210212) has been released. We have implemented FEM computations for MEG and EEG based on the [duneuro](http://duneuro.org) software. Plus fixes to leadfield and Phase-Amplitude-Coupling computations! Many thanks to [Tibo](https://github.com/tiborauer), [Sophie](https://github.com/s-schrader) and [Maria-Carla](https://github.com/mcpiastra)!. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20210128...20210212) for the detailled list of updates.
FieldTrip version [20210212](http://github.com/fieldtrip/fieldtrip/releases/tag/20210212) has been released. We have implemented FEM computations for MEG and EEG based on the [duneuro](http://duneuro.org) software. Plus fixes to leadfield and Phase-Amplitude-Coupling computations! Many thanks to [Tibo](https://github.com/tiborauer), [Sophie](https://github.com/s-schrader) and [Maria-Carla](https://github.com/mcpiastra)!. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20210128...20210212) for the detalled list of updates.
3 changes: 1 addition & 2 deletions _posts/2021-03-25-release.md
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Expand Up @@ -6,5 +6,4 @@ tweet: FieldTrip version 20210325 was just released with improvements to our MVP

### 25 March, 2021

FieldTrip version [20210325](http://github.com/fieldtrip/fieldtrip/releases/tag/20210325) has been released. It features an improved interface to the MVPA-light toolbox thanks to [Matthias Treder](https://github.com/treder). Also, our clustering code has been refrubished to be more generic for univariate data of arbitrary dimensionality. In addition, we have now implementated threshold-free cluster enhancement (TFCE) for multiple comparison correction. This versions also contains various small improvements to figure handling, printing and source functions. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20210311...20210325) for the detailed list of updates.

FieldTrip version [20210325](http://github.com/fieldtrip/fieldtrip/releases/tag/20210325) has been released. It features an improved interface to the MVPA-light toolbox thanks to [Matthias Treder](https://github.com/treder). Also, our clustering code has been refurbished to be more generic for univariate data of arbitrary dimensionality. In addition, we have now implemented threshold-free cluster enhancement (TFCE) for multiple comparison correction. This versions also contains various small improvements to figure handling, printing and source functions. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20210311...20210325) for the detailed list of updates.
2 changes: 1 addition & 1 deletion _posts/2021-05-05-release.md
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Expand Up @@ -8,4 +8,4 @@ tweet: FieldTrip version 20210505 was just released with improved support for ha

FieldTrip version [20210505](http://github.com/fieldtrip/fieldtrip/releases/tag/20210505) has been released with improved support for handling of fMRI time series data! The idea is to convert a 4D fMRI representation into a source representation, and from there into a parcellated raw data representation from which it would be straight-forward to use the time-domain analysis methods :). An example for this is given on the corresponding [getting started](/getting_started/fmri) page.

In addition, we updated [ft_datatype_parcellation](/reference/utilities/ft_datatype_parcellation) and [ft_datatype_segmentation](/reference/utilities/ft_datatype_segmentation) and added suppport for [Polhemus](https://polhemus.com/motion-tracking/all-trackers/liberty) motion capture recordings. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20210422...20210505) for the detailed list of updates.
In addition, we updated [ft_datatype_parcellation](/reference/utilities/ft_datatype_parcellation) and [ft_datatype_segmentation](/reference/utilities/ft_datatype_segmentation) and added support for [Polhemus](https://polhemus.com/motion-tracking/all-trackers/liberty) motion capture recordings. See [GitHub](https://github.com/fieldtrip/fieldtrip/compare/20210422...20210505) for the detailed list of updates.
2 changes: 1 addition & 1 deletion _posts/2021-09-12-release.md
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---
title: 12 September 2021 - FieldTrip version 20210912 has been released
categories: [release]
tweet: FieldTrip version 20210912 was just released was improved coordinate system handling for DICOM/NIFTI, new parcellation-based clustering funcitonality and many more fixes. See http://www.fieldtriptoolbox.org/#12-september-2021
tweet: FieldTrip version 20210912 was just released was improved coordinate system handling for DICOM/NIFTI, new parcellation-based clustering functionality and many more fixes. See http://www.fieldtriptoolbox.org/#12-september-2021
---

### 12 September, 2021
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