The name of the output file. If the length of the raw data exceeds the 2-GByte fif file limit, several output files will be produced. These additional ‘extension’ files will be tagged with
_001.fif
,_002.fif
, etc.
--evoked
Produce and evoked-response fif file instead of a raw data file. Each trial in the CTF data file is included as a separate category (condition). The maximum number of samples in each trial is limited to 25000.
--infoonly
Write only the measurement info to the output file, do not include data.
During conversion, the following files are consulted from the ds directory:
`` <name> .res4``
This file contains most of the header information pertaining the acquisition.
`` <name> .hc``
This file contains the HPI coil locations in sensor and head coordinates.
`` <name> .meg4``
This file contains the actual MEG data. If the data are split across several files due to the 2-GByte file size restriction, the ‘extension’ files are called <name>
.
<number>_meg4
.
`` <name> .eeg``
This is an optional input file containing the EEG electrode locations. More details are given below.
If the <name> .eeg
file,
produced from the Polhemus data file with CTF software, is present,
it is assumed to contain lines with the format:
<number> <name> <x/cm> <y/cm> <z/cm>
The field <number> is
a sequential number to be assigned to the converted data point in
the fif file. <name> is either
a name of an EEG channel, one of left
, right
,
or nasion
to indicate a fiducial landmark, or any word
which is not a name of any channel in the data. If <name> is
a name of an EEG channel available in the data, the location is
included in the Polhemus data as an EEG electrode locations and
inserted as the location of the EEG electrode. If the name is one
of the fiducial landmark names, the point is included in the Polhemus
data as a fiducial landmark. Otherwise, the point is included as
an additional head surface points.
The standard eeg
file produced by CTF software
does not contain the fiducial locations. If desired, they can be
manually copied from the pos
file which was the source
of the eeg
file.
Note
In newer CTF data the EEG position information maybe present in the res4
file. If the eeg
file is present, the positions given there take precedence over the information in the res4
file.
Note
mne_ctf2fiff converts both epoch mode and continuous raw data file into raw data fif files. It is not advisable to use epoch mode files with time gaps between the epochs because the data will be discontinuous in the resulting fif file with jumps at the junctions between epochs. These discontinuities produce artifacts if the raw data is filtered in mne_browse_raw , mne_process_raw , or graph .
Note
The conversion process includes a transformation from the CTF head coordinate system convention to that used in the Neuromag systems.
mne_ctf_dig2fiff¶
The input data to mne_ctf_dig2fiff is
a text file, which contains the coordinates of the digitization
points in centimeters. The first line should contain a single number
which is the number of points listed in the file. Each of the following
lines contains a sequential number of the point, followed by the
three coordinates. mne_ctf_dig2fiff ignores
any text following the \(z\) coordinate
on each line. If the --numfids
option is specified,
the first three points indicate the three fiducial locations (1
= nasion, 2 = left auricular point, 3 = right auricular point).
Otherwise, the input file must end with three lines beginning with left
, right
,
or nasion
to indicate the locations of the fiducial
landmarks, respectively.
Note
The sequential numbers should be unique within a file. I particular, the numbers 1, 2, and 3 must not be appear more than once if the --numfids
options is used.
The command-line options for mne_ctf_dig2fiff are:
--dig <*name*>
Specifies the input data file in CTF output format.
--numfids
Fiducial locations are numbered instead of labeled, see above.
--hpts <*name*>
Specifies the output hpts file. The format of this text file is described in The hpts format.
--fif <*name*>
Specifies the output fif file.
mne_edf2fiff¶
The mne_edf2fiff allows conversion of EEG data from EDF, EDF+, and BDF formats to the fif format. Documentation for these three input formats can be found at:
EDF:
EDF+:
BDF:
EDF (European Data Format) and EDF+ are 16-bit formats while BDF is a 24-bit variant of this format used by the EEG systems manufactured by a company called BioSemi.
None of these formats support electrode location information and head shape digitization information. Therefore, this information has to be provided separately. Presently hpts and elp file formats are supported to include digitization data. For information on these formats, see The hpts format and http://www.sourcesignal.com/formats_probe.html. Note that it is mandatory to have the three fiducial locations (nasion and the two auricular points) included in the digitization data. Using the locations of the fiducial points the digitization data are converted to the MEG head coordinate system employed in the MNE software, see The head and device coordinate systems. In the comparison of the channel names only the initial segment up to the first ‘-‘ (dash) in the EDF/EDF+/BDF channel name is significant.
The EDF+ files may contain an annotation channel which can
be used to store trigger information. The Time-stamped Annotation
Lists (TALs) on the annotation data can be converted to a trigger
channel (STI 014) using an annotation map file which associates
an annotation label with a number on the trigger channel. The TALs
can be listed with the --listtal
option,
see below.
Warning
The data samples in a BDF file are represented in a 3-byte (24-bit) format. Since 3-byte raw data buffers are not presently supported in the fif format these data will be changed to 4-byte integers in the conversion. Since the maximum size of a fif file is 2 GBytes, the maximum size of a BDF file to be converted is approximately 1.5 GBytes
Warning
The EDF/EDF+/BDF formats support channel dependent sampling rates. This feature is not supported by mne_edf2fiff . However, the annotation channel in the EDF+ format can have a different sampling rate. The annotation channel data is not included in the fif files output.
Using mne_edf2fiff¶
The command-line options of mne_edf2fiff are:
--edf <*filename*>
Specifies the name of the raw data file to process.
--tal <*filename*>
List the time-stamped annotation list (TAL) data from an EDF+ file here. This output is useful to assist in creating the annotation map file, see the
--annotmap
option, below. This output file is an event file compatible with mne_browse_raw and mne_process_raw , see Browsing raw data with mne_browse_raw. In addition, in the mapping between TAL labels and trigger numbers provided by the--annotmap
option is employed to assign trigger numbers in the event file produced. In the absence of the--annotmap
option default trigger number 1024 is used.
--annotmap <*filename*>
Specify a file which maps the labels of the TALs to numbers on a trigger channel (STI 014) which will be added to the output file if this option is present. This annotation map file may contain comment lines starting with the ‘%’ or ‘#’ characters. The data lines contain a label-number pair, separated by a colon. For example, a line ‘Trigger-1:9’ means that each annotation labeled with the text ‘Trigger-1’ will be translated to the number 9 on the trigger channel.
--elp <*filename*>
Specifies the name of the an electrode location file. This file is in the “probe” file format used by the Source Signal Imaging, Inc. software. For description of the format, see http://www.sourcesignal.com/formats_probe.html. Note that some other software packages may produce electrode-position files with the elp ending not conforming to the above specification. As discussed above, the fiducial marker locations, optional in the “probe” file format specification are mandatory for mne_edf2fiff . When this option is encountered on the command line any previously specified hpts file will be ignored.
--hpts <*filename*>
Specifies the name of an electrode position file in the hpts format discussed in The hpts format. The mandatory entries are the fiducial marker locations and the EEG electrode locations. It is recommended that electrode (channel) names instead of numbers are used to label the EEG electrode locations. When this option is encountered on the command line any previously specified elp file will be ignored.
--meters
Assumes that the digitization data in an hpts file is given in meters instead of millimeters.
--fif <*filename*>
Specifies the name of the fif file to be output.
Post-conversion tasks¶
This section outlines additional steps to be taken to use the EDF/EDF+/BDF file is converted to the fif format in MNE:
Some of the channels may not have a digitized electrode location associated with them. If these channels are used for EOG or EMG measurements, their channel types should be changed to the correct ones using the mne_rename_channels utility, EEG channels which do not have a location associated with them should be assigned to be MISC channels.
After the channel types are correctly defined, a topographical layout file can be created for mne_browse_raw and mne_analyze using the mne_make_eeg_layout utility.
The trigger channel name in BDF files is “Status”. This must be specified with the
--digtrig
option or with help of the MNE_TRIGGER_CH_NAME environment variable when mne_browse_raw or mne_process_raw is invoked.Only the two least significant bytes on the “Status” channel of BDF files are significant as trigger information the
--digtrigmask
0xff option MNE_TRIGGER_CH_MASK environment variable should be used to specify this to mne_browse_raw and mne_process_raw,
mne_epochs2mat¶
The utility mne_epochs2mat converts epoch data including all or selected channels from a raw data file to a simple binary file with an associated description file in Matlab mat file format. With help of the description file, a matlab program can easily read the epoch data from the simple binary file. Signal space projection and bandpass filtering can be optionally applied to the raw data prior to saving the epochs.
Note
The MNE Matlab toolbox described in MNE-MATLAB toolbox provides direct access to raw fif files without conversion with mne_epochs2mat first. Therefore, it is recommended that you use the Matlab toolbox rather than mne_epochs2mat which creates large files occupying disk space unnecessarily. An exception to this is the case where you apply a filter to the data and save the band-pass filtered epochs.
Command-line options¶
mne_epochs2mat accepts the following command-line options are:
--raw <*name*>
Specifies the name of the raw data fif file to use as input.
--mat <*name*>
Specifies the name of the destination file. Anything following the last period in the file name will be removed before composing the output file name. The binary epoch file will be called <trimmed name>
.epochs
and the corresponding Matlab description file will be <trimmed name>_desc.mat
.
--tag <*tag*>
By default, all Matlab variables included in the description file start with
mne\_
. This option changes the prefix to <tag> _.
--events <*name*>
The file containing the event definitions. This can be a text or fif format file produced by mne_process_raw or mne_browse_raw. With help of this file it is possible to select virtually any data segment from the raw data file. If this option is missing, the digital trigger channel in the raw data file or a fif format event file produced automatically by mne_process_raw or mne_browse_raw is consulted for event information.
--event <*name*>
Event number identifying the epochs of interest.
--tmin <*time/ms*>
The starting point of the epoch with respect to the event of interest.
--tmax <*time/ms*>
The endpoint of the epoch with respect to the event of interest.
--sel <*name*>
Specifies a text file which contains the names of the channels to include in the output file, one channel name per line. If the
--inv
option is specified,--sel
is ignored. If neither--inv
nor--sel
is present, all MEG and EEG channels are included. The digital trigger channel can be included with the--includetrig
option, described below.
--inv <*name*>
Specifies an inverse operator, which will be employed in two ways. First, the channels included to output will be those included in the inverse operator. Second, any signal-space projection operator present in the inverse operator file will be applied to the data. This option cancels the effect of
--sel
and--proj
options.
--digtrig <*name*>
Name of the composite digital trigger channel. The default value is ‘STI 014’. Underscores in the channel name will be replaced by spaces.
--digtrigmask <*number*>
Mask to be applied to the trigger channel values before considering them. This option is useful if one wants to set some bits in a don’t care state. For example, some finger response pads keep the trigger lines high if not in use, i.e., a finger is not in place. Yet, it is convenient to keep these devices permanently connected to the acquisition system. The number can be given in decimal or hexadecimal format (beginning with 0x or 0X). For example, the value 255 (0xFF) means that only the lowest order byte (usually trigger lines 1 - 8 or bits 0 - 7) will be considered.
--includetrig
Add the digital trigger channel to the list of channels to output. This option should not be used if the trigger channel is already included in the selection specified with the
--sel
option.
--filtersize <*size*>
Adjust the length of the FFT to be applied in filtering. The number will be rounded up to the next power of two. If the size is \(N\), the corresponding length of time is \(^N/_{f_s}\), where \(f_s\) is the sampling frequency of your data. The filtering procedure includes overlapping tapers of length \(^N/_2\) so that the total FFT length will actually be \(2N\). The default value is 4096.
--highpass <*value/Hz*>
Highpass filter frequency limit. If this is too low with respect to the selected FFT length and data file sampling frequency, the data will not be highpass filtered. You can experiment with the interactive version to find the lowest applicable filter for your data. This value can be adjusted in the interactive version of the program. The default is 0, i.e., no highpass filter in effect.
--highpassw <*value/Hz*>
The width of the transition band of the highpass filter. The default is 6 frequency bins, where one bin is \(^{f_s}/_{(2N)}\).
--lowpass <*value/Hz*>
Lowpass filter frequency limit. This value can be adjusted in the interactive version of the program. The default is 40 Hz.
--lowpassw <*value/Hz*>
The width of the transition band of the lowpass filter. This value can be adjusted in the interactive version of the program. The default is 5 Hz.
--filteroff
Do not filter the data.
--proj <*name*>
Include signal-space projection (SSP) information from this file. If the
--inv
option is present,--proj
has no effect.
Note
Baseline has not been subtracted from the epochs. This has to be done in subsequent processing with Matlab if so desired.
Note
Strictly speaking, trigger mask value zero would mean that all trigger inputs are ignored. However, for convenience, setting the mask to zero or not setting it at all has the same effect as 0xFFFFFFFF, i.e., all bits set.
Note
The digital trigger channel can also be set with the MNE_TRIGGER_CH_NAME environment variable. Underscores in the variable value will not be replaced with spaces by mne_browse_raw or mne_process_raw . Using the --digtrig
option supersedes the MNE_TRIGGER_CH_NAME environment variable.
Note
The digital trigger channel mask can also be set with the MNE_TRIGGER_CH_MASK environment variable. Using the --digtrigmask
option supersedes the MNE_TRIGGER_CH_MASK environment variable.
The binary epoch data file¶
mne_epochs2mat saves the epoch data extracted from the raw data file is a simple binary file. The data are stored as big-endian single-precision floating point numbers. Assuming that each of the total of \(p\) epochs contains \(n\) channels and \(m\) time points, the data \(s_{jkl}\) are ordered as
where the first index stands for the time point, the second for the channel, and the third for the epoch number, respectively. The data are not calibrated, i.e., the calibration factors present in the Matlab description file have to be applied to get to physical units as described below.
Note
The maximum size of an epoch data file is 2 Gbytes, i.e., 0.5 Gsamples.
Matlab data structures¶
The Matlab description files output by mne_epochs2mat contain a data structure <tag>_epoch_info . The fields of the this structure are listed in The fields of the raw data info structure.. Further explanation of the epochs member is provided in The epochs member of the raw data info structure..
Variable |
Size |
Description |
orig_file |
string |
The name of the original fif file specified with the
|
epoch_file |
string |
The name of the epoch data file produced by mne_epocs2mat. |
nchan |
1 |
Number of channels. |
nepoch |
1 |
Total number of epochs. |
epochs |
nepoch x 5 |
Description of the content of the epoch data file, see The epochs member of the raw data info structure.. |
sfreq |
1 |
The sampling frequency in Hz. |
lowpass |
1 |
Lowpass filter frequency (Hz) |
highpass |
1 |
Highpass filter frequency (Hz) |
ch_names |
nchan (string) |
String array containing the names of the channels included |
ch_types |
nchan x 2 |
The column lists the types of the channels (1 = MEG, 2 = EEG). The second column lists the coil types, see Normal coil descriptions. and Accurate coil descriptions. For EEG electrodes, this value equals one. |
ch_lognos |
nchan x 1 |
Logical channel numbers as listed in the fiff file |
ch_units |
nchan x 2 |
Units and unit multipliers as listed in the fif file. The unit of the data is listed in the first column (T = 112, T/m = 201, V = 107). At present, the second column will be always zero, i.e., no unit multiplier. |
ch_pos |
nchan x 12 |
The location information for each channel. The first three values specify the origin of the sensor coordinate system or the location of the electrode. For MEG channels, the following nine number specify the x, y, and z-direction unit vectors of the sensor coordinate system. For EEG electrodes the first vector after the electrode location specifies the location of the reference electrode. If the reference is not specified this value is all zeroes. The remaining unit vectors are irrelevant for EEG electrodes. |
ch_cals |
nchan x 2 |
The raw data output by mne_raw2mat are not calibrated. The first column is the range member of the fiff data structures and while the second is the cal member. To get calibrated data values in the units given in ch_units from the raw data, the data must be multiplied with the product of range and cal . |
meg_head_trans |
4 x 4 |
The coordinate frame transformation from the MEG device coordinates to the MEG head coordinates. |
Column |
Contents |
1 |
The raw data type (2 or 16 = 2-byte signed integer, 3 = 4-byte signed integer, 4 = single-precision float). The epoch data are written using the big-endian byte order. The data are stored sample by sample. |
2 |
Byte location of this epoch in the binary epoch file. |
3 |
First sample of this epoch in the original raw data file. |
4 |
First sample of the epoch with respect to the event. |
5 |
Number of samples in the epoch. |
Note
For source modelling purposes, it is recommended that the MNE Matlab toolbox, see MNE-MATLAB toolbox is employed to read the measurement info instead of using the channel information in the raw data info structure described in The fields of the raw data info structure..
mne_evoked_data_summary¶
Print a summary of evoked-response data sets in a file (averages only).
--in <name>
The input file.
mne_eximia2fiff¶
Usage:
mne_eximia2fiff
[--dig
dfile ] [--orignames
] file1 file2 …
where file1 file2 …
are eXimia nxe
files and the --orignames
option
is passed on to mne_brain_vision2fiff.
If you want to convert all data files in a directory, say
mne_eximia2fiff *.nxe
The optional file specified with the --dig
option is assumed
to contain digitizer data from the recording in the Nexstim format.
The resulting fif data file will contain these data converted to
the fif format as well as the coordinate transformation between
the eXimia digitizer and MNE head coordinate systems.
Note
This script converts raw data files only.
mne_fit_sphere_to_surf¶
Purpose¶
The utility mne_fit_sphere_to_surf finds the sphere which best fits a given surface.
Command line options¶
mne_fit_sphere_to_surf accepts the following command-line options:
--bem <*name*>
A BEM file to use. The names of these files usually end with
bem.fif
orbem-sol.fif
.
--surf <*name*>
A FreeSurfer surface file to read. This is an alternative to using a surface from the BEM file.
--scalp
Use the scalp surface instead of the inner skull surface in sphere fitting. If the surface is specified with the
--surf
option, this one is irrelevant.
--mritrans <*name*>
A file containing a transformation matrix between the MEG head coordinates and MRI coordinates. With this option, the sphere origin will be output in MEG head coordinates. Otherwise the output will be in MRI coordinates.
mne_fix_mag_coil_types¶
The purpose of mne_fix_mag_coil_types is to change coil type 3022 to 3024 in the MEG channel definition records in the data files specified on the command line.
As shown in Tables 5.2 and 5.3, the Neuromag Vectorview systems can contain magnetometers with two different coil sizes (coil types 3022 and 3023 vs. 3024). The systems incorporating coils of type 3024 were introduced last. At some sites the data files have still defined the magnetometers to be of type 3022 to ensure compatibility with older versions of Neuromag software. In the MNE software as well as in the present version of Neuromag software coil type 3024 is fully supported. Therefore, it is now safe to upgrade the data files to use the true coil type.
If the --magnes
option is specified, the 4D
Magnes magnetometer coil type (4001) is changed to 4D Magnes gradiometer
coil type (4002). Use this option always and only
if your Magnes data comes from a system with axial gradiometers
instead of magnetometers. The fif converter included with the Magnes
system does not assign the gradiometer coil type correctly.
Note
The effect of the difference between the coil sizes of magnetometer types 3022 and 3024 on the current estimates computed by the MNE software is very small. Therefore the use of mne_fix_mag_coil_types is not mandatory.
mne_fix_stim14¶
Some earlier versions of the Neuromag acquisition software had a problem with the encoding of the eighth bit on the digital stimulus channel STI 014. This problem has been now fixed. Old data files can be fixed with mne_fix_stim14 , which takes raw data file names as arguments. mne_fix_stim14 also changes the calibration of STI 014 to unity. If the encoding of STI 014 is already correct, running mne_fix_stim14 will not have any effect on the raw data.
In newer Neuromag Vectorview systems with 16-bit digital
inputs the upper two bytes of the samples may be incorrectly set
when stimulus input 16 is used and the data are acquired in the
32-bit mode. This problem can be fixed by running mne_fix_stim14 on
a raw data file with the --32
option:
mne_fix_stim14 --32
<raw data file>
In this case, the correction will be applied to the stimulus channels ‘STI101’ and ‘STI201’.
mne_flash_bem¶
--help
Prints the usage information.
--usage
Prints the usage information.
--noconvert
Skip conversion of the original MRI data. The original data are not needed and the preparatory steps 1.-3. listed below are thus not needed.
--noflash30
The 30-degree flip angle data are not used.
--unwarp <*type*>
Run grad_unwarp with
--unwarp
<type> option on each of the converted data sets.
mne_insert_4D_comp¶
Import Magnes WH3600 reference channel data from a text file.
--in <name>
The name of the fif file containing the helmet data.
--ref <name>
The name of the text file containing the reference channel data.
--out <name>
The output fif file.
mne_kit2fiff¶
The utility mne_kit2fiff was created in collaboration with Alec Maranz and Asaf Bachrach to import their MEG data acquired with the 160-channel KIT MEG system to MNE software.
To import the data, the following input files are mandatory:
The Polhemus data file (elp file) containing the locations of the fiducials and the head-position indicator (HPI) coils. These data are usually given in the CTF/4D head coordinate system. However, mne_kit2fiff does not rely on this assumption. This file can be exported directly from the KIT system.
A file containing the locations of the HPI coils in the MEG device coordinate system. These data are used together with the elp file to establish the coordinate transformation between the head and device coordinate systems. This file can be produced easily by manually editing one of the files exported by the KIT system.
A sensor data file (sns file) containing the locations and orientations of the sensors. This file can be exported directly from the KIT system.
Note
The output fif file will use the Neuromag head coordinate system convention, see The head and device coordinate systems. A coordinate transformation between the CTF/4D head coordinates and the Neuromag head coordinates is included. This transformation can be read with MNE Matlab Toolbox routines, see MNE-MATLAB toolbox.
The following input files are optional:
A head shape data file (hsp file) containing locations of additional points from the head surface. These points must be given in the same coordinate system as that used for the elp file and the fiducial locations must be within 1 mm from those in the elp file.
A raw data file containing the raw data values, sample by sample, as text. If this file is not specified, the output fif file will only contain the measurement info block.
By default mne_kit2fiff includes
the first 157 channels, assumed to be the MEG channels, in the output
file. The compensation channel data are not converted by default
but can be added, together with other channels, with the --type
.
The channels from 160 onwards are designated as miscellaneous input
channels (MISC 001, MISC 002, etc.). The channel names and types
of these channels can be afterwards changed with the mne_rename_channels
utility. In addition, it is possible to synthesize
the digital trigger channel (STI 014) from available analog
trigger channel data, see the --stim
option, below.
The synthesized trigger channel data value at sample \(k\) will
be:
where \(t_p(k)\) are the thresholded from the input channel data d_p(k):
The threshold value \(t\) can
be adjusted with the --stimthresh
option, see below.
mne_kit2fiff accepts the following command-line options:
--elp <*filename*>
The name of the file containing the locations of the fiducials and the HPI coils. This option is mandatory.
--hsp <*filename*>
The name of the file containing the locations of the fiducials and additional points on the head surface. This file is optional.
--sns <*filename*>
The name of file containing the sensor locations and orientations. This option is mandatory.
--hpi <*filename*>
The name of a text file containing the locations of the HPI coils in the MEG device coordinate frame, given in millimeters. The order of the coils in this file does not have to be the same as that in the elp file. This option is mandatory.
--raw <*filename*>
Specifies the name of the raw data file. If this file is not specified, the output fif file will only contain the measurement info block.
--sfreq <*value/Hz*>
The sampling frequency of the data. If this option is not specified, the sampling frequency defaults to 1000 Hz.
--lowpass <*value/Hz*>
The lowpass filter corner frequency used in the data acquisition. If not specified, this value defaults to 200 Hz.
--highpass <*value/Hz*>
The highpass filter corner frequency used in the data acquisition. If not specified, this value defaults to 0 Hz (DC recording).
--out <*filename*>
Specifies the name of the output fif format data file. If this file is not specified, no output is produced but the elp , hpi , and hsp files are processed normally.
--stim <*chs*>
Specifies a colon-separated list of numbers of channels to be used to synthesize a digital trigger channel. These numbers refer to the scanning order channels as listed in the sns file, starting from one. The digital trigger channel will be the last channel in the file. If this option is absent, the output file will not contain a trigger channel.
--stimthresh <*value*>
The threshold value used when synthesizing the digital trigger channel, see above. Defaults to 1.0.
--add <*chs*>
Specifies a colon-separated list of numbers of channels to include between the 157 default MEG channels and the digital trigger channel. These numbers refer to the scanning order channels as listed in the sns file, starting from one.
Note
The mne_kit2fiff utility has not been extensively tested yet.
mne_list_bem¶
The utility mne_list_bem outputs the BEM meshes in text format. The default output data contains the x, y, and z coordinates of the vertices, listed in millimeters, one vertex per line.
The command-line options are:
--bem <*name*>
The BEM file to be listed. The file name normally ends with -bem.fif or -bem-sol.fif .
--out <*name*>
The output file name.
--id <*number*>
Identify the surface to be listed. The surfaces are numbered starting with the innermost surface. Thus, for a three-layer model the surface numbers are: 4 = scalp, 3 = outer skull, 1 = inner skull Default value is 4.
--gdipoli
List the surfaces in the format required by Thom Oostendorp’s gdipoli program. This is also the default input format for mne_surf2bem .
--meters
List the surface coordinates in meters instead of millimeters.
--surf
Write the output in the binary FreeSurfer format.
--xfit
Write a file compatible with xfit. This is the same effect as using the options
--gdipoli
and--meters
together.
mne_list_coil_def¶
List available coil definitions.
--in <def>
Validate a coil definition file.
--out <name>
List the coil definitions to this file (default: stdout).
--type <type>
Coil type to list.
mne_list_proj¶
--in <name>
Input file.
--ascin <name>
Input file.
--exclude <name>
Exclude these channels from the projection (set entries to zero).
--chs <name>
Specify a file which contains a channel selection for the output (useful for graph)
--asc <name>
Text output.
--fif <name>
Fif output.
--lisp <name>
Lisp output.
mne_list_source_space¶
The utility mne_list_source_space outputs the source space information into text files suitable for loading into the Neuromag MRIlab software.
--src <*name*>
The source space to be listed. This can be either the output from mne_make_source_space (*src.fif), output from the forward calculation (*fwd.fif), or the output from the inverse operator decomposition (*inv.fif).
--mri <*name*>
A file containing the transformation between the head and MRI coordinates is specified with this option. This file can be either a Neuromag MRI description file, the output from the forward calculation (*fwd.fif), or the output from the inverse operator decomposition (*inv.fif). If this file is included, the output will be in head coordinates. Otherwise the source space will be listed in MRI coordinates.
--dip <*name*>
Specifies the ‘stem’ for the Neuromag text format dipole files to be output. Two files will be produced: <stem> -lh.dip and <stem> -rh.dip. These correspond to the left and right hemisphere part of the source space, respectively. This source space data can be imported to MRIlab through the File/Import/Dipoles menu item.
--pnt <*name*>
Specifies the ‘stem’ for Neuromag text format point files to be output. Two files will be produced: <stem> -lh.pnt and <stem> -rh.pnt. These correspond to the left and right hemisphere part of the source space, respectively. This source space data can be imported to MRIlab through the File/Import/Strings menu item.
--exclude <*name*>
Exclude the source space points defined by the given FreeSurfer ‘label’ file from the output. The name of the file should end with
-lh.label
if it refers to the left hemisphere and with-rh.label
if it lists points in the right hemisphere, respectively.
--include <*name*>
Include only the source space points defined by the given FreeSurfer ‘label’ file to the output. The file naming convention is the same as described above under the
--exclude
option. Are ‘include’ labels are processed before the ‘exclude’ labels.
--all
Include all nodes in the output files instead of only those active in the source space. Note that the output files will be huge if this option is active.
mne_list_versions¶
The utility mne_list_versions lists
version numbers and compilation dates of all software modules that
provide this information. This administration utility is located
in $MNE_ROOT/bin/admin
, The output from mne_list_versions or
output of individual modules with --version
option
is useful when bugs are reported to the developers of MNE software.
mne_make_cor_set¶
The utility mne_make_cor_set creates a fif format MRI description file optionally including the MRI data using FreeSurfer MRI volume data as input. The command-line options are:
--dir <*directory*>
Specifies a directory containing the MRI volume in COR format. Any previous
--mgh
options are cancelled when this option is encountered.
--withdata
Include the pixel data to the output file. This option is implied with the
--mgh
option.
--mgh <*name*>
An MRI volume volume file in mgh or mgz format. The
--withdata
option is implied with this type of input. Furthermore, the \(T_3\) transformation, the Talairach transformation \(T_4\) from the talairach.xfm file referred to in the MRI volume, and the the fixed transforms \(T_-\) and \(T_+\) will added to the output file. For definition of the coordinate transformations, see MEG/EEG and MRI coordinate systems.
--talairach <*name*>
Take the Talairach transform from this file instead of the one specified in mgh/mgz files.
--out <*name*>
Specifies the output file, which is a fif-format MRI description file.
mne_make_derivations¶
Purpose¶
In mne_browse_raw , channel derivations are defined as linear combinations of real channels existing in the data files. The utility mne_make_derivations reads derivation data from a suitably formatted text file and produces a fif file containing the weights of derived channels as a sparse matrix. Two input file formats are accepted:
A file containing arithmetic expressions defining the derivations and
A file containing a matrix which specifies the weights of the channels in each derivation.
Both of these formats are described in
Command-line options¶
mne_make_derivations recognizes the following command-line options:
--in <*name*>
Specifies a measurement file which contains the EEG electrode locations. This file is not modified.
--inmat <*name*>
Specifies the output file where the layout is stored. Suffix
.lout
is recommended for layout files. mne_analyze and mne_browse_raw look for the custom layout files from the directory$HOME/.mne/lout
.
--trans
Indicates that the file specified with the
--inmat
option contains a transpose of the derivation matrix.
--thresh <*value*>
Specifies the threshold between values to be considered zero and non-zero in the input file specified with the
--inmat
option. The default threshold is \(10^{-6}\).
--out <*name*>
Specifies output fif file to contain the derivation data. The recommended name of the derivation file has the format <\(name\)>
-deriv.fif
.
--list <*name*>
List the contents of a derivation file to standard output. If this option is missing and
--out
is specified, the content of the output file will be listed once it is complete. If neither--list
nor--out
is present, and--in
or--inmat
is specified, the interpreted contents of the input file is listed.
Derivation file formats¶
All lines in the input files starting with the pound sign (#) are considered to be comments. The format of a derivation in a arithmetic input file is:
where <\(name\)> is the name of the derived channel, \(name_k\) are the names of the channels comprising the derivation, and \(w_k\) are their weights. Note that spaces are necessary between the items. Channel names containing spaces must be put in quotes. For example,
EEG-diff = "EEG 003" - "EEG 002"
defines a channel EEG-diff
which is a difference
between EEG 003
and EEG 002
. Similarly,
EEG-der = 3 * "EEG 010" - 2 * "EEG 002"
defines a channel which is three times EEG 010
minus
two times EEG 002
.
The format of a matrix derivation file is:
The combination of the two arithmetic examples, above can be thus represented as:
2 3 "EEG 002" "EEG 003" "EEG 010" EEG-diff -1 1 0 EEG-der -2 0 3
Before a derivation is accepted to use by mne_browse_raw , the following criteria have to be met:
All channels to be combined into a single derivation must have identical units of measure.
All channels in a single derivation have to be of the same kind, e.g., MEG channels or EEG channels.
All channels specified in a derivation have to be present in the currently loaded data set.
The validity check is done when a derivation file is loaded into mne_browse_raw , see Load derivations.
Note
You might consider renaming the EEG channels with descriptive labels related to the standard 10-20 system using the mne_rename_channels utility. This allows you to use standard EEG channel names in the derivations you define as well as in the channel selection files used in mne_browse_raw , see Selection.
mne_make_eeg_layout¶
Purpose¶
Both MNE software (mne_analyze and mne_browse_raw) and Neuromag software (xplotter and xfit) employ text layout files to create topographical displays of MEG and EEG data. While the MEG channel layout is fixed, the EEG layout varies from experiment to experiment, depending on the number of electrodes used and the electrode cap configuration. The utility mne_make_eeg_layout was created to produce custom EEG layout files based on the EEG electrode location information included in the channel description records.
mne_make_eeg_layout uses azimuthal equidistant projection to map the EEG channel locations onto a plane. The mapping consists of the following steps:
A sphere is fitted to the electrode locations and the locations are translated by the location of the origin of the best-fitting sphere.
The spherical coordinates (\(r_k\), \(\theta_k\), and \(\phi_k\)) corresponding to each translated electrode location are computed.
The projected locations \(u_k = R \theta_k \cos{\phi_k}\) and \(v_k = R \theta_k \sin{\phi_k}\) are computed. By default, \(R = 20/{^{\pi}/_2}\), i.e. at the equator (\(\theta = ^{\pi}/_2\)) the multiplier is 20. This projection radius can be adjusted with the
--prad
option. Increasing or decreasing \(R\) makes the spacing between the channel viewports larger or smaller, respectively.A viewport with width 5 and height 4 is placed centered at the projected location. The width and height of the viewport can be adjusted with the
--width
and--height
options
The command-line options are:
--lout <*name*>
Specifies the name of the layout file to be output.
--nofit
Do not fit a sphere to the electrode locations but use a standard sphere center (\(x = y = 0\), and \(z = 40\) mm) instead.
--prad <*value*>
Specifies a non-standard projection radius \(R\), see above.
--width <*value*>
Specifies the width of the viewports. Default value = 5.
--height <*value*>
Specifies the height of the viewports. Default value = 4.
mne_make_morph_maps¶
Prepare the mapping data for subject-to-subject morphing.
--redo
Recompute the morphing maps even if they already exist.
--from <subject>
Compute morphing maps from this subject.
--to <subject>
Compute morphing maps to this subject.
--all
Do all combinations. If this is used without either
--from
or--to
options, morphing maps for all possible combinations are computed. If--from
or--to
is present, only maps between the specified subject and all others are computed.
Note
Because all morphing map files contain maps in both directions, the choice of --from
and --to
options only affect the naming of the morphing map files to be produced. mne_make_morph_maps creates directory $SUBJECTS_DIR/morph-maps
if necessary.
mne_make_uniform_stc¶
The output will have a time range from -100 to 300 ms. There will be one cycle of 5-Hz sine wave, with the peaks at 50 and 150 ms
--src <name>
Source space to use.
--stc <name>
Stc file to produce.
--maxval <value>
Maximum value (at 50 ms, default 10).
--all
Include all points to the output files.
mne_mark_bad_channels¶
This utility adds or replaces information about unusable (bad) channels. The command line options are:
--bad <*filename*>
Specify a text file containing the names of the bad channels, one channel name per line. The names of the channels in this file must match those in the data file exactly. If this option is missing, the bad channel information is cleared.
<*data file name*>
The remaining arguments are taken as data file names to be modified.
mne_morph_labels¶
Morph label files from one brain to another.
--from <*subject*>
Name of the subject for which the labels were originally defined.
--to <*subject*>
Name of the subject for which the morphed labels should be created.
--labeldir <*directory*>
A directory containing the labels to morph.
--prefix <prefix>
Adds <prefix> in the beginning of the output label names. A dash will be inserted between <prefix> and the rest of the name.
--smooth <number>
Apply smoothing with the indicated number of iteration steps (see About smoothing) to the labels before morphing them. This is advisable because otherwise the resulting labels may have little holes in them since the morphing map is not a bijection. By default, two smoothsteps are taken.
As the labels are morphed, a directory with the name of the
subject specified with the --to
option is created under
the directory specified with --labeldir
to hold the
morphed labels.
mne_prepare_bem_model¶
--bem <*name*>
Specify the name of the file containing the triangulations of the BEM surfaces and the conductivities of the compartments. The standard ending for this file is
-bem.fif
and it is produced either with the utility mne_surf2bem (Creating the BEM meshes) or the convenience script mne_setup_forward_model, see Setting up the boundary-element model.
--sol <*name*>
Specify the name of the file containing the triangulation and conductivity information together with the BEM geometry matrix computed by mne_prepare_bem_model . The standard ending for this file is
-bem-sol.fif
.
--method <*approximation method*>
Select the BEM approach. If <approximation method> is
constant
, the BEM basis functions are constant functions on each triangle and the collocation points are the midpoints of the triangles. Withlinear
, the BEM basis functions are linear functions on each triangle and the collocation points are the vertices of the triangulation. This is the preferred method to use. The accuracy will be the same or better than in the constant collocation approach with about half the number of unknowns in the BEM equations.
mne_process_stc¶
--stc <name>
Specify the stc file to process.
--out <name>
Specify a stc output file name.
--outasc <name>
Specify a text output file name.
--scaleto <scale>
Scale the data so that the maximum is this value.
--scaleby <scale>
Multiply the values by this.
mne_raw2mat¶
The utility mne_raw2mat converts all or selected channels from a raw data file to a Matlab mat file. In addition, this utility can provide information about the raw data file so that the raw data can be read directly from the original fif file using Matlab file I/O routines.
Note
The MNE Matlab toolbox described in MNE-MATLAB toolbox provides direct access to raw fif files without a need for conversion to mat file format first. Therefore, it is recommended that you use the Matlab toolbox rather than mne_raw2mat which creates large files occupying disk space unnecessarily.
Command-line options¶
mne_raw2mat accepts the following command-line options:
--raw <*name*>
Specifies the name of the raw data fif file to convert.
--mat <*name*>
Specifies the name of the destination Matlab file.
--info
With this option present, only information about the raw data file is included. The raw data itself is omitted.
--sel <*name*>
Specifies a text file which contains the names of the channels to include in the output file, one channel name per line. If the
--info
option is specified,--sel
does not have any effect.
--tag <*tag*>
By default, all Matlab variables included in the output file start with
mne\_
. This option changes the prefix to <tag> _.
Matlab data structures¶
The Matlab files output by mne_raw2mat can
contain two data structures, <tag>_raw and <tag>_raw_info .
If --info
option is specified, the file contains the
latter structure only.
The <tag>_raw structure contains only one field, data which is a matrix containing the raw data. Each row of this matrix constitutes the data from one channel in the original file. The data type of this matrix is the same of the original data (2-byte signed integer, 4-byte signed integer, or single-precision float).
The fields of the <tag>_raw_info structure are listed in The fields of the raw data info structure.. Further explanation of the bufs field is provided in The bufs member of the raw data info structure..
Variable |
Size |
Description |
orig_file |
string |
The name of the original fif file specified with the
|
nchan |
1 |
Number of channels. |
nsamp |
1 |
Total number of samples |
bufs |
nbuf x 4 |
This field is present if |
sfreq |
1 |
The sampling frequency in Hz. |
lowpass |
1 |
Lowpass filter frequency (Hz) |
highpass |
1 |
Highpass filter frequency (Hz) |
ch_names |
nchan (string) |
String array containing the names of the channels included |
ch_types |
nchan x 2 |
The column lists the types of the channesl (1 = MEG, 2 = EEG). The second column lists the coil types, see Normal coil descriptions. and Accurate coil descriptions. For EEG electrodes, this value equals one. |
ch_lognos |
nchan x 1 |
Logical channel numbers as listed in the fiff file |
ch_units |
nchan x 2 |
Units and unit multipliers as listed in the fif file. The unit of the data is listed in the first column (T = 112, T/m = 201, V = 107). At present, the second column will be always zero, i.e., no unit multiplier. |
ch_pos |
nchan x 12 |
The location information for each channel. The first three values specify the origin of the sensor coordinate system or the location of the electrode. For MEG channels, the following nine number specify the x, y, and z-direction unit vectors of the sensor coordinate system. For EEG electrodes the first vector after the electrode location specifies the location of the reference electrode. If the reference is not specified this value is all zeroes. The remaining unit vectors are irrelevant for EEG electrodes. |
ch_cals |
nchan x 2 |
The raw data output by mne_raw2mat is uncalibrated. The first column is the range member of the fiff data structures and while the second is the cal member. To get calibrared data values in the units given in ch_units from the raw data, the data must be multiplied with the product of range and cal . |
meg_head_trans |
4 x 4 |
The coordinate frame transformation from the MEG device coordinates to the MEG head coordinates. |
Column |
Contents |
1 |
The raw data type (2 or 16 = 2-byte signed integer, 3 = 4-byte signed integer, 4 = single-precision float). All data in the fif file are written in the big-endian byte order. The raw data are stored sample by sample. |
2 |
Byte location of this buffer in the original fif file. |
3 |
First sample of this buffer. Since raw data storing can be switched on and off during the acquisition, there might be gaps between the end of one buffer and the beginning of the next. |
4 |
Number of samples in the buffer. |
mne_rename_channels¶
Sometimes it is necessary to change the names types of channels in MEG/EEG data files. Such situations include:
Designating an EEG as an EOG channel. For example, the EOG channels are not recognized as such in the fif files converted from CTF data files.
Changing the name of the digital trigger channel of interest to STI 014 so that mne_browse_raw and mne_process_raw will recognize the correct channel without the need to specify the
--digtrig
option or the MNE_TRIGGER_CH_NAME environment variable every time a data file is loaded.
The utility mne_rename_channels was designed to meet the above needs. It recognizes the following command-line options:
--fif <*name*>
Specifies the name of the data file to modify.
--alias <*name*>
Specifies the text file which contains the modifications to be applied, see below.
--revert
Reverse the roles of old and new channel names in the alias file.
Each line in the alias file contains the old name and new name for a channel, separated by a colon. The old name is a name of one of the channels presently in the file and the new name is the name to be assigned to it. The old name must match an existing channel name in the file exactly. The new name may be followed by another colon and a number which is the channel type to be assigned to this channel. The channel type options are listed below.
Channel type |
Corresponding number |
|---|---|
MEG |
1 |
MCG |
201 |
EEG |
2 |
EOG |
202 |
EMG |
302 |
ECG |
402 |
MISC |
502 |
STIM |
3 |
Warning
Do not attempt to designate MEG channels to EEG channels or vice versa. This may result in strange errors during source estimation.
Note
You might consider renaming the EEG channels with descriptive labels related to the standard 10-20 system. This allows you to use standard EEG channel names when defining derivations, see mne_make_derivations and Load derivations, as well as in the channel selection files used in mne_browse_raw , see Selection.
mne_sensitivity_map¶
Purpose¶
mne_sensitivity_map computes the size of the columns of the forward operator and outputs the result in w files.
Command line options¶
mne_sensitivity_map accepts the following command-line options:
--fwd <*name*>
Specifies a forward solution file to analyze. By default the MEG forward solution is considered.
--proj <*name*>
Specifies a file containing an SSP operator to be applied. If necessary, multiple
--proj
options can be specified. For map types 1 - 4 (see below), SSP is applied to the forward model data. For map types 5 and 6, the effects of SSP are evaluated against the unmodified forward model.
--eeg
Use the EEG forward solution instead of the MEG one. It does not make sense to consider a combination because of the different units of measure. For the same reason, gradiometers and magnetometers have to be handled separately, see
--mag
option below. By default MEG gradiometers are included.
--mag
Include MEG magnetometers instead of gradiometers
--w <*name*>
Specifies the stem of the output w files. To obtain the final output file names,
-lh.w
and-rh.w
is appended for the left and right hemisphere, respectively.
--smooth <*number*>
Specifies the number of smooth steps to apply to the resulting w files. Default: no smoothing.
--map <*number*>
Select the type of a sensitivity map to compute. At present, valid numbers are 1 - 6. For details, see Available sensitivity maps, below.
Available sensitivity maps¶
In the following, let
denote the three consecutive columns of the gain matrix \(G\) corresponding to the fields of three orthogonal dipoles at source space location \(k\). Further, lets assume that the source coordinate system has been selected so that the \(z\) -axis points to the cortical normal direction and the \(xy\) plane is thus the tangent plane of the cortex at the source space location \(k\) Next, compute the SVD
and let \(g_{1k} = u_{1k} \lambda_{1k}\), where \(\lambda_{1k}\) and \(u_{1k}\) are the largest singular value and the corresponding left singular vector of \(G_k\), respectively. It is easy to see that \(g_{1k}\) is has the largest power among the signal distributions produced by unit dipoles at source space location \(k\).
Furthermore, assume that the columns orthogonal matrix \(U_P\) (\(U_P^T U_P = I\)) contain
the orthogonal basis of the noise subspace corresponding to the signal
space projection (SSP) operator \(P\) specified
with one or more --proj
options so that \(P = I - U_P U_P^T\).
For more information on SSP, see The Signal-Space Projection (SSP) method.
With these definitions the map selections defined with the --map
option correspond
to the following
--map 1
Compute \(\sqrt{g_{1k}^T g_{1k}} = \lambda_{1k}\) at each source space point. Normalize the result so that the maximum values equals one.
--map 2
Compute \(\sqrt{g_z^T g_z}\) at each source space point. Normalize the result so that the maximum values equals one. This is the amplitude of the signals produced by unit dipoles normal to the cortical surface.
--map 3
Compute \(\sqrt{g_z^T g_z / g_{1k}^T g_{1k}}\) at each source space point.
--map 4
Compute \(1 - \sqrt{g_z^T g_z / g_{1k}^T g_{1k}}\) at each source space point. This could be called the radiality index.
--map 5
Compute the subspace correlation between \(g_z\) and \(U_P\): \(\text{subcorr}^2(g_z , U_P) = (g_z^T U_P U_P^T g_z)/(g_z^T g_z)\). This index equals zero, if \(g_z\) is orthogonal to \(U_P\) and one if \(g_z\) lies in the subspace defined by \(U_P\). This map shows how close the field pattern of a dipole oriented perpendicular to the cortex at each cortical location is to the subspace removed by the SSP.
--map 6
Compute \(\sqrt{g_z^T P g_z / g_z^T g_z}\), which is the fraction of the field pattern of a dipole oriented perpendicular to the cortex at each cortical location remaining after applying the SSP a dipole remaining
mne_sensor_locations¶
--meas <name>
Measurement file.
--magonly
Magnetometers only.
--ell
Output sensor ellipsoids for MRIlab.
--dir
Output direction info as well.
--dev
Output in MEG device coordinates.
--out <name>
Name output file
mne_show_fiff¶
Using the utility mne_show_fiff it is possible to display information about the contents of a fif file to the standard output. The command line options for mne_show_fiff are:
--in <*name*>
Specifies the fif file whose contents will be listed.
--verbose
Produce a verbose output. The data of most tags is included in the output. This excludes matrices and vectors. Only the first 80 characters of strings are listed unless the
--long
option is present.
--blocks
Only list the blocks (the tree structure) of the file. The tags within each block are not listed.
--indent <*number*>
Number of spaces for indentation for each deeper level in the tree structure of the fif files. The default indentation is 3 spaces in terse and no spaces in verbose listing mode.
--long
List all data from string tags instead of the first 80 characters. This options has no effect unless the
--verbose
option is also present.
--tag <*number*>
List only tags of this kind. Multiple
--tag
options can be specified to list several different kinds of data.
mne_show_fiff reads the
explanations of tag kinds, block kinds, and units from $MNE_ROOT/share/mne/fiff_explanations.txt
.
mne_simu¶
Purpose¶
The utility mne_simu creates simulated evoked response data for investigation of the properties of the inverse solutions. It computes MEG signals generated by dipoles normal to the cortical mantle at one or several ROIs defined with label files. Colored noise can be added to the signals.
Command-line options¶
mne_simu has the following command-line options:
--fwd <*name*>
Specify a forward solution file to employ in the simulation.
--label <*name*>
Specify a label
--meg
Provide MEG data in the output file.
--eeg
Provide EEG data in the output file.
--out <*name*>
Specify the output file. By default, this will be an evoked data file in the fif format.
--raw
Output the data as a raw data fif file instead of an evoked one.
--mat
Produce Matlab output of the simulated fields instead of the fif evoked file.
--label <*name*>
Define an ROI. Several label files can be present. By default, the sources in the labels will have \(\cos^2\) -shaped non-overlapping timecourses, see below.
--timecourse <*name*>
Specifies a text file which contains an expression for a source time course, see Source waveform expressions. If no –timecourse options are present, the standard source time courses described in Simulated data are used. Otherwise, the time course expressions are read from the files specified. The time course expressions are associated with the labels in the order they are specified. If the number of expressions is smaller than the number of labels, the last expression specified will reused for the remaining labels.
--sfreq <*freq/Hz*>
Specifies the sampling frequency of the output data (default = 1000 Hz). This option is used only with the time course files.
--tmin <*time/ms*>
Specifies the starting time of the data, used only with time course files (default -200 ms).
--tmax <*time/ms*>
Specifies the ending time of the data, used only with time course files (default 500 ms).
--seed <*number*>
Specifies the seed for random numbers. This seed is used both for adding noise, see Noise simulation and for random numbers in source waveform expressions, see Source waveform expressions. If no seed is specified, the current time in seconds since Epoch (January 1, 1970) is used.
--all
Activate all sources on the cortical surface uniformly. This overrides the
--label
options.
Noise simulation¶
Noise is added to the signals if the --senscov
and --nave
options
are present. If --nave
is omitted the number of averages
is set to \(L = 100\). The noise is computed
by first generating vectors of Gaussian random numbers \(n(t)\) with \(n_j(t) \sim N(0,1)\).
Thereafter, the noise-covariance matrix \(C\) is
used to color the noise:
where we have used the eigenvalue decomposition positive-definite covariance matrix:
Note that it is assumed that the noise-covariance matrix is given for raw data, i.e., for \(L = 1\).
Simulated data¶
The default source waveform \(q_k\) for the \(k^{th}\) label is nonzero at times \(t_{kp} = (100(k - 1) + p)/f_s\), \(p = 0 \dotso 100\) with:
i.e., the source waveforms are non-overlapping 100-samples wide \(\cos^2\) pulses. The sampling frequency \(f_s = 600\) Hz. The source amplitude \(Q_k\) is determined so that the strength of each of the dipoles in a label will be \(50 \text{nAm}/N_k\).
Let us denote the sums of the magnetic fields and electric potentials produced by the dipoles normal to the cortical mantle at label \(k\) by \(x_k\). The simulated signals are then:
where \(N_s\) is the number of sources.
Source waveform expressions¶
The --timecourse
option provides flexible possibilities
to define the source waveforms in a functional form. The source
waveform expression files consist of lines of the form:
<variable>
=
<arithmetic expression>
Each file may contain multiple lines. At the end of the evaluation,
only the values in the variable y
(q
)
are significant, see Available variable names in source waveform expressions.. They assume the role
of \(q_k(t_j)\) to compute the simulated signals
as described in Simulated data, above.
All expressions are case insensitive. The variables are vectors
with the length equal to the number of samples in the responses,
determined by the --tmin
, --tmax
, and --sfreq
options.
The available variables are listed in Available variable names in source waveform expressions..
Variable |
Meaning |
|---|---|
x |
time [s] |
t |
current value of x in [ms] |
y |
the source amplitude [Am] |
q |
synonym for y |
a , b , c , d |
help variables, initialized to zeros |
The arithmetic expressions can use usual arithmetic operations as well as mathematical functions listed in Mathematical functions available for source waveform expressions. The arguments can be vectors or scalar numbers. In addition, standard relational operators ( <, >, ==, <=, >=) and their textual equivalents (lt, gt, eq, le, ge) are available. Table Examples of source waveform expressions. gives some useful examples of source waveform expressions.
Function |
Description |
abs(x) |
absolute value |
acos(x) |
\(\cos^{-1}x\) |
asin(x) |
\(\sin^{-1}x\) |
atan(x) |
\(\tan^{-1}x\) |
atan2(x,y) |
\(\tan^{-1}(^y/_x)\) |
ceil(x) |
nearest integer larger than \(x\) |
cos(x) |
\(\cos x\) |
cosw(x,a,b,c) |
\(\cos^2\) -shaped window centered at \(b\) with a rising slope of length \(a\) and a trailing slope of length \(b\). |
deg(x) |
The value of \(x\) converted to from radians to degrees |
erf(x) |
\(\frac{1}{2\pi} \int_0^x{\text{exp}(-t^2)dt}\) |
erfc(x) |
\(1 - \text{erf}(x)\) |
exp(x) |
\(e^x\) |
floor(x) |
Largest integer value not larger than \(x\) |
hypot(x,y) |
\(\sqrt{x^2 + y^2}\) |
ln(x) |
\(\ln x\) |
log(x) |
\(\log_{10} x\) |
maxp(x,y) |
Takes the maximum between \(x\) and \(y\) |
minp(x,y) |
Takes the minimum between \(x\) and \(y\) |
mod(x,y) |
Gives the remainder of \(x\) divided by \(y\) |
pi |
Ratio of the circumference of a circle and its diameter. |
rand |
Gives a vector of uniformly distributed random numbers from 0 to 1. |
rnorm(x,y) |
Gives a vector of Gaussian random numbers distributed as \(N(x,y)\). Note that if \(x\) and \(y\) are vectors, each number generated will a different mean and variance according to the arguments. |
shift(x,s) |
Shifts the values in the input vector \(x\) by the number of positions given by \(s\). Note that \(s\) must be a scalar. |
sin(x) |
\(\sin x\) |
sqr(x) |
\(x^2\) |
sqrt(x) |
\(\sqrt{x}\) |
tan(x) |
\(\tan x\) |
Expression |
Meaning |
q = 20e-9*sin(2*pi*10*x) |
A 10-Hz sine wave with 20 nAm amplitude |
q = 20e-9*sin(2*pi*2*x)*sin(2*pi*10*x) |
A 10-Hz 20-nAm sine wave, amplitude modulated sinusoidally at 2 Hz. |
q = 20e-9*cosw(t,100,100,100) |
\(\cos^2\)-shaped pulse, centered at \(t\) = 100 ms with 100 ms leading and trailing slopes, 20 nAm amplitude |
q = 30e-9*(t > 0)*(t <* 300)*sin(2*pi*20*x) |
20-Hz sine wave, 30 nAm amplitude, cropped in time to 0…300 ms. |
mne_smooth¶
Produce a smoothed version of a w or an stc file
--src <name>
The source space file.
--in <name>
The w or stc file to smooth.
--smooth <val>
Number of smoothsteps
mne_surf2bem¶
--surf <*name*>
Specifies a FreeSurfer binary format surface file. Before specifying the next surface (
--surf
or--tri
options) details of the surface specification can be given with the options listed in Surface options.
--tri <*name*>
Specifies a text format surface file. Before specifying the next surface (
--surf
or--tri
options) details of the surface specification can be given with the options listed in Surface options. The format of these files is described in Tessellation file format.
--check
Check that the surfaces are complete and that they do not intersect. This is a recommended option. For more information, see Topology checks.
--checkmore
In addition to the checks implied by the
--check
option, check skull and skull thicknesses. For more information, see Topology checks.
--fif <*name*>
The output fif file containing the BEM. These files normally reside in the bem subdirectory under the subject’s mri data. A name ending with
-bem.fif
is recommended.
Surface options¶
These options can be specified after each --surf
or --tri
option
to define details for the corresponding surface.
--swap
Swap the ordering or the triangle vertices. The standard convention in the MNE software is to have the vertices ordered so that the vector cross product of the vectors from vertex 1 to 2 and 1 to 3 gives the direction of the outward surface normal. Text format triangle files produced by the some software packages have an opposite order. For these files, the
--swap
. option is required. This option does not have any effect on the interpretation of the FreeSurfer surface files specified with the--surf
option.
--sigma <*value*>
The conductivity of the compartment inside this surface in S/m.
--shift <*value/mm*>
Shift the vertices of this surface by this amount, given in mm, in the outward direction, i.e., in the positive vertex normal direction.
--meters
The vertex coordinates of this surface are given in meters instead of millimeters. This option applies to text format files only. This definition does not affect the units of the shift option.
--id <*number*>
Identification number to assign to this surface. (1 = inner skull, 3 = outer skull, 4 = scalp).
--ico <*number*>
Downsample the surface to the designated subdivision of an icosahedron. This option is relevant (and required) only if the triangulation is isomorphic with a recursively subdivided icosahedron. For example, the surfaces produced by with mri_watershed are isomorphic with the 5th subdivision of a an icosahedron thus containing 20480 triangles. However, this number of triangles is too large for present computers. Therefore, the triangulations have to be decimated. Specifying
--ico 4
yields 5120 triangles per surface while--ico 3
results in 1280 triangles. The recommended choice is--ico 4
.
mne_transform_points¶
Purpose¶
mne_transform_points applies the coordinate transformation relating the MEG head coordinates and the MRI coordinates to a set of locations listed in a text file.
Command line options¶
mne_transform_points accepts the following command-line options:
--in <*name*>
Specifies the input file. The file must contain three numbers on each line which are the x, y, and z coordinates of point in space. By default, the input is in millimeters.
--iso <*name*>
Specifies a name of a fif file containing Isotrak data. If this option is present file will be used as the input instead of the text file specified with the
--in
option.
--trans <*name*>
Specifies the name of a fif file containing the coordinate transformation between the MEG head coordinates and MRI coordinates. If this file is not present, the transformation will be replaced by a unit transform.
--out <*name*>
Specifies the output file. This file has the same format as the input file.
--hpts
Output the data in the head points (hpts) format accepted by tkmedit . In this format, the coordinates are preceded by a point category (hpi, cardinal or fiducial, eeg, extra) and a sequence number, see The hpts format.
--meters
The coordinates are listed in meters rather than millimeters.
--tomri
By default, the coordinates are transformed from MRI coordinates to MEG head coordinates. This option reverses the transformation to be from MEG head coordinates to MRI coordinates.
mne_tufts2fiff¶
--raw <*filename*>
Specifies the name of the raw data file to process.
--cal <*filename*>
The name of the calibration data file. If calibration data are missing, the calibration coefficients will be set to unity.
--elp <*filename*>
The name of the electrode location file. If this file is missing, the electrode locations will be unspecified. This file is in the “probe” file format used by the Source Signal Imaging, Inc. software. For description of the format, see http://www.sourcesignal.com/formats_probe.html. The fiducial marker locations, optional in the “probe” file format specification are mandatory for mne_tufts2fiff . Note that some other software packages may produce electrode-position files with the elp ending not conforming to the above specification.
Note
The conversion process includes a transformation from the Tufts head coordinate system convention to that used in the Neuromag systems.
Note
The fiducial landmark locations, optional in the probe file format, must be present for mne_tufts2fiff .
mne_view_manual¶
This script shows you the manual in a PDF reader.
mne_volume_data2mri¶
With help of the mne_volume_source_space utility
it is possible to create a source space which
is defined within a volume rather than a surface. If the --mri
option
was used in mne_volume_source_space, the
source space file contains an interpolator matrix which performs
a trilinear interpolation into the voxel space of the MRI volume
specified.
The purpose of the mne_volume_data2mri is to produce MRI overlay data compatible with FreeSurfer MRI viewers (in the mgh or mgz formats) from this type of w or stc files.
The command-line options are:
--src <*filename*>
The name of the volumetric source space file created with mne_volume_source_space . The source space must have been created with the
--mri
option, which adds the appropriate sparse trilinear interpolator matrix to the source space.
--w <*filename*>
The name of a w file to convert into an MRI overlay.
--stc <*filename*>
The name of the stc file to convert into an MRI overlay. If this file has many time frames, the output file may be huge. Note: If both
-w
and--stc
are specified,-w
takes precedence.
--scale <*number*>
Multiply the stc or w by this scaling constant before producing the overlay.
--out <*filename*>
Specifies the name of the output MRI overlay file. The name must end with either
.mgh
or.mgz
identifying the uncompressed and compressed FreeSurfer MRI formats, respectively.
mne_volume_source_space¶
--surf <*name*>
Specifies a FreeSurfer surface file containing the surface which will be used as the boundary for the source space.
--bem <*name*>
Specifies a BEM file (ending in
-bem.fif
). The inner skull surface will be used as the boundary for the source space.
--origin <*x/mm*> : <*y/mm*> : <*z/mm*>
If neither of the two surface options described above is present, the source space will be spherical with the origin at this location, given in MRI (RAS) coordinates.
--rad <*radius/mm*>
Specifies the radius of a spherical source space. Default value = 90 mm
--grid <*spacing/mm*>
Specifies the grid spacing in the source space.
--mindist <*distance/mm*>
Only points which are further than this distance from the bounding surface are included. Default value = 5 mm.
--exclude <*distance/mm*>
Exclude points that are closer than this distance to the center of mass of the bounding surface. By default, there will be no exclusion.
--mri <*name*>
Specifies a MRI volume (in mgz or mgh format). If this argument is present the output source space file will contain a (sparse) interpolation matrix which allows mne_volume_data2mri to create an MRI overlay file, see mne_volume_data2mri.
--pos <*name*>
Specifies a name of a text file containing the source locations and, optionally, orientations. Each line of the file should contain 3 or 6 values. If the number of values is 3, they indicate the source location, in millimeters. The orientation of the sources will be set to the z-direction. If the number of values is 6, the source orientation will be parallel to the vector defined by the remaining 3 numbers on each line. With
--pos
, all of the options defined above will be ignored. By default, the source position and orientation data are assumed to be given in MRI coordinates.
--head
If this option is present, the source locations and orientations in the file specified with the
--pos
option are assumed to be given in the MEG head coordinates.
--meters
Indicates that the source locations in the file defined with the
--pos
option are give in meters instead of millimeters.
--src <*name*>
Specifies the output file name. Use a name * <dir>/ <name>*-src.fif
--all
Include all vertices in the output file, not just those in use. This option is implied when the
--mri
option is present. Even with the--all
option, only those vertices actually selected will be marked to be “in use” in the output source space file.
mne_watershed_bem¶
--subject <*subject*>
Defines the name of the subject. This can be also accomplished by setting the SUBJECT environment variable.
--overwrite
Overwrite the results of previous run of mne_watershed_bem .
--atlas
Makes mri_watershed to employ atlas information to correct the segmentation.


library(tidylsr)
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
A minimal example for the two sample test:
iris %>%
filter(Species != "versicolor") %>%
ttest_twosample(Sepal.Length ~ Species)
#>
#> Welch's two sample t-test
#>
#> Variables:
#> outcome: Sepal.Length
#> group: Species
#>
#> Descriptives:
#> sample mean sd
#> setosa 5.006 0.352
#> virginica 6.588 0.636
#>
#> Hypotheses:
#> null: population means are equal
#> alternative: population means are different
#>
#> Test results:
#> t-statistic: -15.386
#> degrees of freedom: 76.516
#> p-value: <.001
#>
#> 95% confidence interval:
#> lower bound: -1.787
#> upper bound: -1.377
A minimal example for the one sample test:
iris %>%
filter(Species == "virginica") %>%
ttest_onesample(outcome = Sepal.Length, null_mean = 6)
#>
#> One sample t-test
#>
#> Variables:
#> outcome: Sepal.Length
#>
#> Descriptives:
#> sample mean sd
#> Sepal.Length 6.588 0.636
#>
#> Hypotheses:
#> null: population mean equals 6
#> alternative: population mean not equal to 6
#>
#> Test results:
#> t-statistic: 6.539
#> degrees of freedom: 49
#> p-value: <.001
#>
#> 95% confidence interval:
#> lower bound: 6.407
#> upper bound: 6.769


Community
Mailing list
Subscribe to the UltraSuite mailing list to get updates from the UltraSuite repository and to send and receive messages from other UltraSuite users.
The UltraSuite mailing list can be found at:
http://lists.inf.ed.ac.uk/mailman/listinfo/ultrasuite
To post to this list (subscribers only), send your email to<EMAIL_ADDRESS>If you ever want to unsubscribe or change your options (e.g. switch to or from digest mode, change your password, etc.), visit your subscription page at:
http://lists.inf.ed.ac.uk/mailman/options/ultrasuite/yourname@yourmail
You can also make such adjustments via email by sending a message to:
<EMAIL_ADDRESS>with the word ‘help’ in the subject or body (don’t include the quotes), and you will get back a message with instructions.
Publications
This is a list of work describing, using, or referencing the data available in the Ultrasuite repository.
Database papers
- Ribeiro, M. S., Sanger, J., Zhang, J.-X., Eshky, A., Wrench, A., Richmond, K.,& Renals, S. (2021). TaL: a synchronised multi-speaker corpus of ultrasound tongue imaging, audio, and lip videos. Proceedings of the IEEE Workshop on Spoken Language Technology (SLT). Shenzhen, China.[Paper]
- Eshky, A., Ribeiro, M. S., Cleland, J., Richmond, K., Roxburgh, Z., Scobbie, J., & Wrench, A. (2018) Ultrasuite: A repository of ultrasound and acoustic data from child speech therapy sessions. Proceedings of INTERSPEECH. Hyderabad, India. [Paper]
Applications
- Csapó, T. G., & Xu, K. (2020). Quantification of Transducer Misalignment in Ultrasound Tongue Imaging. Proc. Interspeech.[Paper] [Code]
- Zhu, J., Styler, W., & Calloway, I. (2020) MTracker-a CNN-based tool for automatic tracking of tongue contours. UltraFest, Indiana, USA. [Paper] [Code]
- Zhu, J., Styler, W., & Calloway, I. (2019). A CNN-based tool for automatic tongue contour tracking in ultrasound images. arXiv preprint arXiv:1907.10210. [Paper] [Code]
- Eshky, A., Ribeiro, M. S., Richmond, K., & Renals, S. (2019). Synchronising audio and ultrasound by learning cross-modal embeddings. Proc. Interspeech. Graz, Austria. [Paper] [Code].
- Ribeiro, M. S., Eshky, A., Richmond, K., & Renals, S. (2019). Ultrasound tongue imaging for diarization and alignment of child speech therapy sessions. Proc. Interspeech. Graz, Austria. [Paper] [Code]
- Ribeiro, M. S., Eshky, A., Richmond, K., & Renals, S. (2019). Speaker-independent classification of phonetic segments from raw ultrasound in child speech. In ICASSP 2019-2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (pp. 1328-1332). [Paper].
- Shahin, M., Ahmed, B., Smith, D. V., Duenser, A., & Epps, J. (2019). Automatic Screening of Children with Speech Sound Disorders Using Paralinguistic Features. In IEEE 29th International Workshop on Machine Learning for Signal Processing (MLSP) (pp. 1-5).[Paper (not open access)].
- Shahin, M., Zafar, U., & Ahmed, B. (2019). The Automatic Detection of Speech Disorders in Children: Challenges, Opportunities, and Preliminary Results. IEEE Journal of Selected Topics in Signal Processing, 14(2), 400-412. [Paper (not open access)].
- Ribeiro, M. S., Eshky, A., Richmond, K., & Renals, S. (2018). Towards robust word alignment of child speech therapy sessions. UK Speech, Dublin, Ireland. [Abstract] [Poster]
References
- Mozaffari, M. H., Sankoff, D., & Lee, W. S. (2019). Ultrasound tongue contour extraction using BowNet network: A deep learning approach. In Proceedings of Meetings on Acoustics 178, ASA (Vol. 39, No. 1, p. 020001). Acoustical Society of America. [Paper]
- Mozaffari, M. H., Ratul, M., Rab, A., & Lee, W. S. (2019). Irisnet: Deep learning for automatic and real-time tongue contour tracking in ultrasound video data using peripheral vision. arXiv preprint arXiv:1911.03972.
- Hewer, A., Steiner, I., & Richmond, K. (2019). Analysis of coarticulation using EMA data with a statistical shape space model of the tongue. Studientexte zur Sprachkommunikation: Elektronische Sprachsignalverarbeitung 2019, 296-303. [Paper].
- Scobbie, J. M., & Ma, J. (2019). Say again? Individual articulatory strategies for producing a clearly-spoken minimal pair wordlist. Proc. 19th ICPhS. [Paper]
Publications list last update: November 2020


If you have diabetes then I recommend uninstalling the app. The app works by frequently entering into Bluetooth scan mode to collect tracing data from other covidsafe users. On some phones this will cause existing connections to drop.https://t.co/DJYiIPGAlo
— geoffrey huntley (@GeoffreyHuntley) May 2, 2020
***Important information for CGM Users***
— Diabetes Australia (@DiabetesAus) April 30, 2020
We have received reports from a number of people with diabetes who have downloaded the Australian Government COVIDSafe app to their smartphone and have experienced connection problems with their continuous glucose monitoring (CGM) apps.
Now, on the topic of @DiabetesAus. It sounds like there's bugs in the CGM apps that they don't alarm for loss of connectivity.
— geoffrey huntley (@GeoffreyHuntley) May 2, 2020
Now, if these apps were opensource we could validate this suspicion easily. @shanselman says it best over at https://t.co/5Mo0ENsx0m
And this varies hugely between phones (e.g. my Pixel 2 can scan, advertise, and talk to my headphones all at the same time). But not all controllers can do everything concurrently, and it's even more complicated if you consider dual-stack (i.e. BT classic concurrently with BLE).
— Jim Mussared (@jim_mussared) May 2, 2020


| Class Summary | |
sealed trait
|
BooleanW
extends AnyRef
Wraps
scala.Boolean and provides additional methods. |
sealed trait
|
CharSet
extends AnyRef
|
sealed trait
|
Digit
extends AnyRef
A digit from 0 to 9.
|
sealed trait
|
Effect
extends AnyRef
A wrapper around a side-effect (
scala.Unit ) |
sealed trait
|
EitherW
[+A, +B] extends AnyRef
Wraps
scala.Either and provides additional methods. |
sealed trait
|
Equal
[A] extends AnyRef
Equality between two values that serves as a suitable replacement for (the defective)
java.lang.Object.equals . |
sealed trait
|
EqualW
[A] extends AnyRef
Wraps an argument of
Equal implementations. |
sealed trait
|
ListW
[A] extends AnyRef
Wraps
scala.List and provides additional methods. |
sealed trait
|
OptionW
[A] extends AnyRef
Wraps
scala.Option and provides additional methods. |
sealed trait
|
Order
[A] extends AnyRef
Order between two values.
|
sealed trait
|
Ordering
extends AnyRef
An ordering of 'less than', 'equal to' or 'greater than'.
|
trait
|
PartialType
[T, A] extends AnyRef
Applies one type argument of two. This is used for taking a type constructor of kind
* -> * -> * to
* -> * by partially applying one type argument. The Apply type applies the first argument
and the Flip type applies the second argument. See also
Ticket #339. |
trait
|
PartialType2
[T, A] extends AnyRef
Applies one type argument of two where one of the type arguments has a kind * -> *.
|
sealed trait
|
Proxy
[A] extends AnyRef
A type-constructor for a lifted value.
|
trait
|
Show
[A] extends AnyRef
A strategy for displaying a value that serves as a suitable replacement for (the defective)
java.lang.Object.toString . |
sealed trait
|
State
[S, +A] extends AnyRef
Stateful computation.
|
sealed trait
|
StringW
extends AnyRef
Wraps
scala.Predef.String and provides additional methods. |
| Object Summary | |
object
|
BooleanW
extends AnyRef
Functions over boolean values.
|
object
|
CharSet
extends AnyRef
|
object
|
Digit
extends AnyRef
Functions over digits.
|
case object
|
EQ
extends Ordering with scala.Product
An ordering of 'equal to'.
|
object
|
Effect
extends AnyRef
Functions over side-effects.
|
object
|
EitherW
extends AnyRef
Functions over either values.
|
object
|
Equal
extends AnyRef
Functions over equality.
|
object
|
EqualW
extends AnyRef
Functions over equal wrapper values.
|
case object
|
GT
extends Ordering with scala.Product
An ordering of 'greater than'.
|
case object
|
LT
extends Ordering with scala.Product
An ordering of 'less than'.
|
object
|
ListW
extends AnyRef
Functions over list values.
|
object
|
OptionW
extends AnyRef
Functions over option values.
|
object
|
Order
extends AnyRef
Functions over order.
|
object
|
Ordering
extends AnyRef
Functions over ordering.
|
object
|
Proxy
extends AnyRef
Functions over proxies.
|
object
|
Show
extends AnyRef
Functions over show.
|
object
|
State
extends AnyRef
Functions over state.
|
object
|
StringW
extends AnyRef
Functions over strings.
|
object
|
Version
extends scala.Application
Prints the version of this software.
|
case object
|
_0
extends Digit with scala.Product
Zero.
|
case object
|
_1
extends Digit with scala.Product
One.
|
case object
|
_2
extends Digit with scala.Product
Two.
|
case object
|
_3
extends Digit with scala.Product
Three.
|
case object
|
_4
extends Digit with scala.Product
Four.
|
case object
|
_5
extends Digit with scala.Product
Five.
|
case object
|
_6
extends Digit with scala.Product
Six.
|
case object
|
_7
extends Digit with scala.Product
Seven.
|
case object
|
_8
extends Digit with scala.Product
Eight.
|
case object
|
_9
extends Digit with scala.Product
Nine.
|


This is p1. It has no explicit bg colour so should be rgb(219, 131, 125). baby-span1 - A span with no bg colour set, so will be colour of parent (rgb(219, 131, 125))
This is p2. It has a bg colour of rgb(125, 214, 219). baby-span2 - A span with no bg colour set, so will be colour of parent (rgb(125, 214, 219)) baby-span3 - A span with its own bg colour set, so will be rgb(206, 125, 219) rather than colour of parent


I'm an aspiring web developer currently enrolled in the University of Washington Coding Full Stack Web Development Boot Camp with a passion for making responsive, user-friendly websites. I am well-organized and collaborative with a strong work ethic, bringing creativity from a background in hospitality and event management. When I’m not attending class or studying, I enjoy cooking, traveling, reading, playing the world’s only 10-player arcade game Killer Queen, and spending time with friends and family. Upon completion of the boot camp I’m looking forward to the opportunity to apply my new skills in the non-profit field.


Hangman Game
Use the alphabet below to guess the word.
Sorry, your browser does not support inline SVG.
8
New Game
Do not ask for confirm when the game is about to be reset.


Toggle navigation
Garden Assist
Dashboard
Garden Central
Dashboard
--%
Remaining
--°C
Current Temperature
Moisture Readings


This report describes the ISO TC211 codelist catalogs, the codelists they contain, and the values and definitions of the codes.
Please contact Ted Habermann if you have questions or suggestions.
| Entry | Definition |
|---|---|
| loose | service instance is loosely coupled with a data instance, i.e. no MD_DataIdentification class has to be described |
| mixed | service instance is mixed coupled with a data instance, i.e. MD_DataIdentification describes the associated data instance and additionally the service instance might work with other external data instances |
| tight | service instance is tightly coupled with a data instance, i.e. MD_DataIdentification class MUST be described |
| Entry | Definition |
|---|---|
| in | the parameter is an input parameter to the service instance |
| out | the parameter is an output parameter to the service instance |
| in/out | the parameter is both an input and output parameter to the service instance |


{% extends "baselayout.html" %} {% block content %}
Welcome to the Sign Search section of the {{langauge}} SignBank. Here you can search for a sign using an English keyword in the search box above, or browse keywords starting with any letter below.
Enter English word or first few letters:
Or search alphabetically:
{% for letter in "ABCDEFGHIJKLMNOPQRSTUVWXYZ" %} {{letter}} | {% endfor %}


|
|
| $_contentIdKey = '' |
| |
|
| $_contentRoute = '' |
| |
|
| $_contentTypePhraseKey = '' |
| |
◆ __construct()
◆ _canUploadAndManageAttachments()
| _canUploadAndManageAttachments |
( |
array |
$contentData, |
|
|
array |
$viewingUser |
|
) |
| |
|
abstractprotected |
Determines if the specified user can upload new attachments or manage existing ones. The content data may contain different type-specific values in different situations. Eg, when posting a thread, only the node_id is known; when posting a reply, the thread_id is know; when editing a post, the post_id is known.
- Parameters
-
| array | $contentData | Type-specific params based on context |
| array | $viewingUser | Viewing user array |
- Returns
- boolean
◆ _canViewAttachment()
| _canViewAttachment |
( |
array |
$attachment, |
|
|
array |
$viewingUser |
|
) |
| |
|
abstractprotected |
Determines if the specified user can view the given attachment.
- Parameters
-
| array | $attachment | Attachment to view |
| array | $viewingUser | Viewing user array |
- Returns
- boolean
◆ attachmentPostDelete()
| attachmentPostDelete |
( |
array |
$attachment, |
|
|
Zend_Db_Adapter_Abstract |
$db |
|
) |
| |
|
abstract |
Behavior to carry out after deleting an attachment (such as reducing an attachment count on the content). This is only called when the attachment has been associated with particular content (not just uploaded unassociated).
- Parameters
-
| array | $attachment | Attachment that has been deleted |
| Zend_Db_Adapter_Abstract | $db | DB object |
◆ canUploadAndManageAttachments()
| canUploadAndManageAttachments |
( |
array |
$contentData, |
|
|
array |
$viewingUser = null |
|
) |
| |
|
final |
Determines if the specified user can upload new attachments or manage existing ones. The content data may contain different type-specific values in different situations. Eg, when posting a thread, only the node_id is known; when posting a reply, the thread_id is know; when editing a post, the post_id is known.
- Parameters
-
| array | $contentData | Type-specific params based on context |
| array | null | $viewingUser | Viewing user array; null for visitor |
- Returns
- boolean
◆ canViewAttachment()
| canViewAttachment |
( |
array |
$attachment, |
|
|
array |
$viewingUser = null |
|
) |
| |
|
final |
Determines if the specified user can view the given attachment.
- Parameters
-
| array | $attachment | Attachment to view |
| array | null | $viewingUser | Viewing user array; null for visitor |
- Returns
- boolean
◆ getAttachmentConstraints()
| getAttachmentConstraints |
( |
| ) |
|
Get attachment constraints for the current attachment content type
- Returns
- array
◆ getAttachmentCountLimit()
| getAttachmentCountLimit |
( |
| ) |
|
Returns the maximum allowed attachments for this content type.
- Returns
- integer|true If true, there is no limit
◆ getContentDataFromContentId()
| getContentDataFromContentId |
( |
|
$contentId | ) |
|
Builds a content data array. By default, this only contains only the primary content ID.
- Parameters
-
- Returns
- array
◆ getContentIdFromContentData()
| getContentIdFromContentData |
( |
array |
$contentData | ) |
|
Gets the primary content ID from an array of content data, if provided.
- Parameters
-
| array | $contentData | Type-specific content data |
- Returns
- integer
◆ getContentLink()
| getContentLink |
( |
array |
$attachment, |
|
|
array |
$extraParams = array() , |
|
|
|
$skipPrepend = false |
|
) |
| |
Builds a link to the host content for an attachment
- Parameters
-
| array | $attachment | data - ideally containing everything necessary to build the content link |
| array | $extraParams | |
| boolean | $skipPrepend | |
- Returns
- string
◆ getContentTypePhraseKey()
| getContentTypePhraseKey |
( |
| ) |
|
Returns the phrase key of a phrase that names the content type managed by this handler.
- Returns
- string
◆ standardizeViewingUserReference()
| standardizeViewingUserReference |
( |
array & |
$viewingUser = null | ) |
|
Standardizes the viewing user array reference.
- Parameters
-
| array | null | $viewingUser | Viewing user array. Will be normalized. |
The documentation for this class was generated from the following file:
- C:/Users/Michel/Desktop/test/xf/library/XenForo/AttachmentHandler/Abstract.php


--- layout: base ---
from dropin import SimplePipeline, RavelPreProcessor, CorrelationModel
import numpy as np
im = np.random.randn(5, 100, 100) > 1
RavelPreProcessor.fit_transform(im).sum(axis=1)/100
autocorrelation_result = CorrelationModel(sz=(100,100), s=(150, 150,)).fit_transform(im);
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
plt.pcolor(np.fft.fftshift(autocorrelation_result[0]));
pip install -r requirements-dev.txt
python setup.py develop
watchmedo tricks tricks.yaml
The watchmedo
script will convert your notebooks to scripts and html files. py.test-ipynb
will test all notebooks matching test-*.ipynb
.
jekyll serve docs -wit
Docs are hosted at http://localhost:4000/magical-magic/
.
surfs-up
is released as free software under the BSD 3-Clause license.


Your organisation
You have been invited to join a collaborative application for the competition Technology Inspired.
Lead organisation: Worth Systems
Lead applicant: John Smith
The lead applicant has invited you to join this application on behalf of the following organisation: Nomensa
If this is not the correct organisation email the application lead


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| Aircraft Compartment Measurement Id | System.Guid |
| Length | System.Decimal |
| Height | System.Decimal |
| Width | System.Decimal |
| Payload In Kilo | System.Decimal |
| Unit Load Device Positions | System.Int32 |
| Carry On Bin Count | System.Int32 |
| Carry On Pieces Allowed Count | System.Int32 |
| Carry On Piece Max Weight In Kilo | System.Int32 |
| Infant Limit | System.Int32 |
| Bookable Limit | System.Int32 |
| Passenger Limit | System.Int32 |
| Row Count | System.Int32 |
| Column Count | System.Int32 |
| User Id | System.Guid |
| Date Time | System.DateTime |


--- layout: post title: "Where is the algorithm on Mastodon" permalink: /:title/ tags: [mastodon] ---
On Twitter national security and political view are expressed by many of those I follow, and today many are moving to mastodon. Last night while auditioning mastodon as a Twitter replacement, I was feeling I did not get the information I desired all the posts etc. Mastodon is not heavy on the recommendation engine, if there is one, and you are more in control of what you see in your Home feed. You are the algorithm.
About 15 years ago I was frustrated with Facebook why did it send me stuff and how do I find that stuff again. On Facebook the users are the product, your attention is marketed to advertisers.
In the past I have used Twitter to review releases of other long form information web postings from government and companies. I would follow those entities and get the latest information to review.
The MAGA King choose Twitter as the platform of 2016 to 2021. I began to follow top MAGA media figures and anti MAGA sources. 2017 was a difficult transition, members of my family and acquaintances had been radicalized by the MAGA world, some were at the conspiratorial stage. Eventually I found a series of sources to follow based on my interests in legal, national security, military and government policies, and Twitter became hot. I liked what the Twitter algorithm sent to me during 2020. My review of these events, now in 2022, seems to support the view that the Facebook and Twitter algorithms were part of the outrage machine that entered the global discourse in 2015.
Twitter has had a difficult time being profitable. The Billionaire Rocketman purchased Twitter with a billion dollar non-refundable deal, he then sued in Delaware and lost. His first efforts were to drag the Twitter machinery through the sandy mud by firing people by email and then regretting is a few days later. The people I value on Twitter started joining mastodon.
My conclusion this morning is on Mastodon we build our own suggestion feed. This has implications for many of us. On Twitter I would often ignore many of the thread comments, how do even see these on Mastodon. Are there comment threads?
This post has been edited on October 13, 2022


|
Cow Country Classic Road Race SUNDAY JUNE 5, 2005 - WOLF CREEK, MONTANA
|
|
DIRECTIONS:
Register and stage at the Holter Lake Road fishing access parking area located 3 miles northeast of Wolf Creek on “Recreation Road”.
SCHEDULE:
8:30 – 9:30AM - Registration 9:45 AM ‑ Mandatory Racers Meeting 10:00 AM ‑ Senior 1,2,3 Start 10:10 AM – Men 4/5 Start 10:20 AM – Masters 40+ Start 10:30 AM – Women, Juniors, Masters 55+ Start
RULES:
Centerline rule will be enforced, including at the finish. Neutral zone in Wolf Creek for all racers. All USA Cycling Rules apply. Racers MUST obey all traffic laws. Helmets are mandatory for all racers.
ENTRY FEES:
Race day registration only $20 Entry Fee, includes insurance surcharge Juniors pay only insurance surcharge $10 One-day licenses available at registration
CONTACT/INFORMATION:
Byron DeFord at<PHONE_NUMBER> Great Divide Cyclery at<PHONE_NUMBER> |
|
PRIZES - Minimum $400 CASH + Prizes Sr. Men 1/2 - $150, Sr. Men 3 - $70 Sr. Men 4/5 - $50, Jr. Men - Prizes Sr. Women - $50 Masters 40+ - $50, Masters 55+ - $30 (Promoter reserves right to combine categories) |
|
|
|
SAVE TIME ON RACE DAY AND FILL OUT THE RELEASE FORM IN ADVANCE: #http://www.usacycling.org/forms/rider_release.pdf
|


Java Collections Framework is very rich with features, it is designed for representing and manipulating the collections, helps developer with providing many inbuilt features, function to manage data.
It has got many advantages as listed below:
Java Collections framework has got many interfaces which we can use based on our required implementation, like Collection, Set, List, Map, Queue, Dequeue, Iterator, SortedSet, SortedMap etc


Reload
Name:
name
LV:
lv
Reload to preprocess sources
Mission
Reload to preprocess sources
Build
Reload to preprocess sources
Repair
Reload to preprocess sources
Decks
Ships
Docks
Items
Columns
Filters
Poppy lock:
locked
dup
Levels:
-
ShipType:
All
None
建造名称
Reload to preprocess sources
Reload to preprocess sources
Reload to preprocess sources
test field


Revision information:
Global tests result:
Minimum code coverage:
| File name: | Pass / fail | Functions | Functions and exits | Statement blocks | Implicit blocks | Decisions | Loops | Basic conditions | Modified conditions | Multiple conditions |
| File name: | Pass / fail | Functions | Functions and exits | Statement blocks | Implicit blocks | Decisions | Loops | Basic conditions | Modified conditions | Multiple conditions |


| Methods' Details |
| registerScriptEvent
|
| registerScriptEvents
|
revokeScriptEvent
| void |
| revokeScriptEvent( |
[in] long |
nIndex, |
| [in] string |
aListenerType, |
| [in] string |
aEventMethod, |
| [in] string |
aRemoveListenerParam ) |
| raises( |
::com::sun::star::lang::IllegalArgumentException ); |
- Description
- revokes the registration of an event.
The parameters ListenerType and
EventMethod are equivalent to the first two
members of the ScriptEventDescriptor
used to register events. If this event at this index has
been attached to any object, it is detached automatically
(see attach).
Exceptions of type
::com::sun::star::beans::IntrospectionException and
CannotCreateAdapterException
that can be thrown by methods of XEventAttacher are caught
and ignored.
- See also
- attach
|
|
revokeScriptEvents
- Description
- revokes all events which are registered for the given index.
If the events at this index have been attached to any
object, they are detached automatically.
(see attach).
- See also
- attach
|
|
insertEntry
- Description
- creates an empty entry at the given position.
The index n of all entries with n >=
nIndex will be increased by one.
|
|
removeEntry
- Description
- removes the entry at the given position.
If any events are registered at this index, they will
be revoked, too. So if the events at this index have been
attached to any object they are detached automatically.
(see attach).
- See also
- attach
|
|
getScriptEvents
- Description
- @eturns
all events registered for the given object index.
- Parameter Index
- an index previously inserted with the method insertEntry.
- Throws
- IllegalArgumentException
if Index is not valid.
|
|
| attach
|
| detach
|
| addScriptListener
|
removeScriptListener
- Description
- removes a XScriptListener from the listener list.
Nothing happens if the listener is not registered.
It is suggested to allow multiple registration of the same listener,
thus for each time a listener is added, it has to be removed.
- See also
- addScriptListener
|
|
Copyright © 2013, The Apache Software Foundation, Licensed under the Apache License, Version 2.0. Apache, the Apache feather logo, Apache OpenOffice and OpenOffice.org are trademarks of The Apache Software Foundation. Other names may be trademarks of their respective owners.