Command line tools using Python#
mne anonymize#
Anonymize raw fif file.#
Usage: mne anonymize [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -f FILE, --file=FILE
Name of file to modify.
- -o OUTFILE, --output=OUTFILE
Name of anonymized output file.`anon-` prefix is added to FILE if not given
- --keep_his
Keep the HIS tag (not advised)
- -d N_DAYS, --daysback=N_DAYS
Move dates in file backwards by this many days.
- --overwrite
Overwrite input file.
To anonymize other file types call mne.io.anonymize_info()
on their
Info
objects and resave to disk.
Examples#
$ mne anonymize -f sample_audvis_raw.fif
mne browse_raw#
Browse raw data.#
Usage: mne browse_raw raw [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- --raw=FILE
Input raw FIF file (can also be specified directly as an argument without the –raw prefix)
- --proj=FILE
Projector file
- --projoff
Disable all projectors
- --eve=FILE
Events file
- -d DURATION, --duration=DURATION
Time window for plotting (s)
- -t START, --start=START
Initial start time for plotting
- -n N_CHANNELS, --n_channels=N_CHANNELS
Number of channels to plot at a time
- -o GROUP_BY, --order=GROUP_BY
Order to use for grouping during plotting (‘type’ or ‘original’)
- -p, --preload
Preload raw data (for faster navigaton)
- -s SHOW_OPTIONS, --show_options=SHOW_OPTIONS
Show projection options dialog
- --allowmaxshield
Allow loading MaxShield processed data
- --highpass=HIGHPASS
Display high-pass filter corner frequency
- --lowpass=LOWPASS
Display low-pass filter corner frequency
- --filtorder=FILTORDER
Display filtering IIR order (or 0 to use FIR)
- --clipping=CLIPPING
Enable trace clipping mode, either ‘clamp’ or ‘transparent’
- --filterchpi
Enable filtering cHPI signals.
- --verbose
Enable verbose mode (printing of log messages).
This uses mne.io.read_raw()
so it supports the same formats
(without keyword arguments).
Examples#
$ mne browse_raw sample_audvis_raw.fif \
--proj sample_audvis_ecg-proj.fif \
--eve sample_audvis_raw-eve.fif
mne bti2fiff#
Import BTi / 4D MagnesWH3600 data to fif file.#
Usage: mne bti2fiff [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -p FILE, --pdf=FILE
Input data file name
- -c FILE, --config=FILE
Input config file name
- --head_shape=FILE
Headshape file name
- -o OUT_FNAME, --out_fname=OUT_FNAME
Name of the resulting fiff file
- -r ROTATION_X, --rotation_x=ROTATION_X
Compensatory rotation about Neuromag x axis, deg
- -T TRANSLATION, --translation=TRANSLATION
Default translation, meter
- --ecg_ch=ECG_CH
4D ECG channel name
- --eog_ch=EOG_CH
4D EOG channel names
Notes#
Currently direct inclusion of reference channel weights is not supported. Please use 'mne_create_comp_data' to include the weights or use the low level functions from this module to include them by yourself.
The informed guess for the 4D name is E31 for the ECG channel and E63, E63 for the EOG channels. Please check and adjust if those channels are present in your dataset but ‘ECG 01’ and ‘EOG 01’, ‘EOG 02’ don’t appear in the channel names of the raw object.
Examples#
$ mne bti2fiff --pdf C,rfDC -o my_raw.fif
mne clean_eog_ecg#
Clean a raw file from EOG and ECG artifacts with PCA (ie SSP).#
Usage: mne clean_eog_ecg [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -i FILE, --in=FILE
Input raw FIF file
- -o FILE, --out=FILE
Output raw FIF file
- -e, --no-eog
Remove EOG
- -c, --no-ecg
Remove ECG
- -q, --quiet
Suppress mne_process_raw output
Examples#
$ mne clean_eog_ecg -i in_raw.fif -o clean_raw.fif -e -c
mne compare_fiff#
Compare FIFF files.#
Usage: mne compare_fiff <file_a> <file_b>
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
Examples#
$ mne compare_fiff test_raw.fif test_raw_sss.fif
mne compute_proj_ecg#
Compute SSP/PCA projections for ECG artifacts.#
Usage: mne compute_proj_ecg [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -i FILE, --in=FILE
Input raw FIF file
- --tmin=TMIN
Time before event in seconds
- --tmax=TMAX
Time after event in seconds
- -g N_GRAD, --n-grad=N_GRAD
Number of SSP vectors for gradiometers
- -m N_MAG, --n-mag=N_MAG
Number of SSP vectors for magnetometers
- -e N_EEG, --n-eeg=N_EEG
Number of SSP vectors for EEG
- --l-freq=L_FREQ
Filter low cut-off frequency in Hz
- --h-freq=H_FREQ
Filter high cut-off frequency in Hz
- --ecg-l-freq=ECG_L_FREQ
Filter low cut-off frequency in Hz used for ECG event detection
- --ecg-h-freq=ECG_H_FREQ
Filter high cut-off frequency in Hz used for ECG event detection
- -p PRELOAD, --preload=PRELOAD
Temporary file used during computation (to save memory)
- -a, --average
Compute SSP after averaging
- --proj=PROJ
Use SSP projections from a fif file.
- --filtersize=FILTER_LENGTH
Number of taps to use for filtering
- -j N_JOBS, --n-jobs=N_JOBS
Number of jobs to run in parallel
- -c CH_NAME, --channel=CH_NAME
Channel to use for ECG detection (Required if no ECG found)
- --rej-grad=REJ_GRAD
Gradiometers rejection parameter in fT/cm (peak to peak amplitude)
- --rej-mag=REJ_MAG
Magnetometers rejection parameter in fT (peak to peak amplitude)
- --rej-eeg=REJ_EEG
EEG rejection parameter in µV (peak to peak amplitude)
- --rej-eog=REJ_EOG
EOG rejection parameter in µV (peak to peak amplitude)
- --avg-ref
Add EEG average reference proj
- --no-proj
Exclude the SSP projectors currently in the fiff file
- --bad=BAD_FNAME
Text file containing bad channels list (one per line)
- --event-id=EVENT_ID
ID to use for events
- --event-raw=RAW_EVENT_FNAME
raw file to use for event detection
- --tstart=TSTART
Start artifact detection after tstart seconds
- --qrsthr=QRS_THRESHOLD
QRS detection threshold. Between 0 and 1. Can also be ‘auto’ for automatic selection
Examples#
$ mne compute_proj_ecg -i sample_audvis_raw.fif -c "MEG 1531" -a \
--l-freq 1 --h-freq 100 \
--rej-grad 3000 --rej-mag 4000 --rej-eeg 100
mne compute_proj_eog#
Compute SSP/PCA projections for EOG artifacts.#
Usage: mne compute_proj_eog [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -i FILE, --in=FILE
Input raw FIF file
- --tmin=TMIN
Time before event in seconds
- --tmax=TMAX
Time after event in seconds
- -g N_GRAD, --n-grad=N_GRAD
Number of SSP vectors for gradiometers
- -m N_MAG, --n-mag=N_MAG
Number of SSP vectors for magnetometers
- -e N_EEG, --n-eeg=N_EEG
Number of SSP vectors for EEG
- --l-freq=L_FREQ
Filter low cut-off frequency in Hz
- --h-freq=H_FREQ
Filter high cut-off frequency in Hz
- --eog-l-freq=EOG_L_FREQ
Filter low cut-off frequency in Hz used for EOG event detection
- --eog-h-freq=EOG_H_FREQ
Filter high cut-off frequency in Hz used for EOG event detection
- -p PRELOAD, --preload=PRELOAD
Temporary file used during computation (to save memory)
- -a, --average
Compute SSP after averaging
- --proj=PROJ
Use SSP projections from a fif file.
- --filtersize=FILTER_LENGTH
Number of taps to use for filtering
- -j N_JOBS, --n-jobs=N_JOBS
Number of jobs to run in parallel
- --rej-grad=REJ_GRAD
Gradiometers rejection parameter in fT/cm (peak to peak amplitude)
- --rej-mag=REJ_MAG
Magnetometers rejection parameter in fT (peak to peak amplitude)
- --rej-eeg=REJ_EEG
EEG rejection parameter in µV (peak to peak amplitude)
- --rej-eog=REJ_EOG
EOG rejection parameter in µV (peak to peak amplitude)
- --avg-ref
Add EEG average reference proj
- --no-proj
Exclude the SSP projectors currently in the fiff file
- --bad=BAD_FNAME
Text file containing bad channels list (one per line)
- --event-id=EVENT_ID
ID to use for events
- --event-raw=RAW_EVENT_FNAME
raw file to use for event detection
- --tstart=TSTART
Start artifact detection after tstart seconds
- -c CH_NAME, --channel=CH_NAME
Custom EOG channel(s), comma separated
Examples#
$ mne compute_proj_eog -i sample_audvis_raw.fif -a \
--l-freq 1 --h-freq 35 \
--rej-grad 3000 --rej-mag 4000 --rej-eeg 100
or
$ mne compute_proj_eog -i sample_audvis_raw.fif -a \
--l-freq 1 --h-freq 35 \
--rej-grad 3000 --rej-mag 4000 --rej-eeg 100 \
--proj sample_audvis_ecg-proj.fif
to exclude ECG artifacts from projection computation.
mne coreg#
Open the coregistration GUI.#
Usage: mne coreg [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR
Subjects directory
- -s SUBJECT, --subject=SUBJECT
Subject name
- -f INST, --fiff=INST
FIFF file with digitizer data for coregistration
- -t, --tabbed
Option for small screens: Combine the data source panel and the coregistration panel into a single panel with tabs.
- --no-guess-mri
Prevent the GUI from automatically guessing and changing the MRI subject when a new head shape source file is selected.
- --head-opacity=HEAD_OPACITY
The opacity of the head surface, in the range [0, 1].
- --high-res-head
Use a high-resolution head surface.
- --low-res-head
Use a low-resolution head surface.
- --trans=TRANS
Head<->MRI transform FIF file (“-trans.fif”)
- --interaction=INTERACTION
Interaction style to use, can be “trackball” or “terrain”.
- --scale=SCALE
Scale factor for the scene.
- --simple-rendering
Use simplified OpenGL rendering
- --verbose
Enable verbose mode (printing of log messages).
Examples#
$ mne coreg
mne flash_bem#
Create 3-layer BEM model from Flash MRI images.#
Usage: mne flash_bem [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s SUBJECT, --subject=SUBJECT
Subject name
- -d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR
Subjects directory
- -3, --flash30, --noflash30
The 30-degree flip angle data. If no argument do not use flash30. If arguments are given, them as file names.
- -5, --flash5
Path to the multiecho flash 5 images. Can be one file or one per echo.
- -r, --registered
Set if the Flash MRI images have already been registered with the T1.mgz file.
- -n, --noconvert
[DEPRECATED] Assume that the Flash MRI images have already been converted to mgz files
- -u, --unwarp
Run grad_unwarp with -unwarp <type> option on each of the converted data sets
- -o, --overwrite
Write over existing .surf files in bem folder
- -v, --view
Show BEM model in 3D for visual inspection
- --copy
Use copies instead of symlinks for surfaces
- -p FLASH_PATH, --flash-path=FLASH_PATH
[DEPRECATED] The directory containing flash5.mgz files (defaults to $SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps
Examples#
$ mne flash_bem --subject=sample
$ mne flash_bem -s sample -n --registered -5 sample/mri/mef05.mgz -3 sample/mri/mef30.mgz
$ mne flash_bem -s sample -n --registered -5 sample/mri/flash/mef05_*.mgz -3 sample/mri/flash/mef30_*.mgz
Notes#
This program assumes that FreeSurfer and MNE are installed and sourced properly.
This function extracts the BEM surfaces (outer skull, inner skull, and outer skin) from multiecho FLASH MRI data with spin angles of 5 and 30 degrees. The multiecho FLASH data can be input as .mgz or .nii files. This function assumes that the Freesurfer segmentation of the subject has been completed. In particular, the T1.mgz and brain.mgz MRI volumes should be, as usual, in the subject’s mri directory.
mne freeview_bem_surfaces#
View the 3-Layers BEM model using Freeview.#
Usage: mne freeview_bem_surfaces [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s SUBJECT, --subject=SUBJECT
Subject name
- -d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR
Subjects directory
- -m METHOD, --method=METHOD
Method used to generate the BEM model. Can be flash or watershed.
Examples#
$ mne freeview_bem_surfaces -s sample
mne kit2fiff#
Import KIT / NYU data to fif file.#
Usage: mne kit2fiff [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- --input=filename
Input data file name
- --mrk=filename
MEG Marker file name
- --elp=filename
Headshape points file name
- --hsp=filename
Headshape file name
- --stim=chs
Colon Separated Stimulus Trigger Channels
- --slope=slope
Slope direction
- --stimthresh=value
Threshold value for trigger channels
- --output=filename
Name of the resulting fiff file
- --debug
Set logging level for terminal output to debug
Examples#
$ mne kit2fiff --input input.sqd --output output.fif
Use without arguments to invoke GUI:
$ mne kt2fiff
mne make_scalp_surfaces#
Create high-resolution head surfaces for coordinate alignment.#
Usage: mne make_scalp_surfaces [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -o, --overwrite
Overwrite previously computed surface
- -s SUBJECT, --subject=SUBJECT
The name of the subject
- -m MRI, --mri=MRI
The MRI file to process using mkheadsurf.
- -f, --force
Force creation of the surface even if it has some topological defects.
- -t THRESHOLD, --threshold=THRESHOLD
Threshold value to use with the MRI.
- -d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR
Subjects directory
- -n, --no-decimate
Disable medium and sparse decimations (dense only)
- --verbose
Enable verbose mode (printing of log messages).
Examples#
$ mne make_scalp_surfaces --overwrite --subject sample
mne maxfilter#
Apply MaxFilter.#
Usage: mne maxfilter [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -i FILE, --in=FILE
Input raw FIF file
- -o FILE
Output FIF file (if not set, suffix ‘_sss’ will be used)
- --origin=ORIGIN
Head origin in mm, or a filename to read the origin from. If not set it will be estimated from headshape points
- --origin-out=ORIGIN_OUT
Filename to use for computed origin
- --frame=FRAME
Coordinate frame for head center (‘device’ or ‘head’)
- --bad=BAD
List of static bad channels
- --autobad=AUTOBAD
Set automated bad channel detection (‘on’, ‘off’, ‘n’)
- --skip=SKIP
Skips raw data sequences, time intervals pairs in s, e.g.: 0 30 120 150
- --force
Ignore program warnings
- --st
Apply the time-domain MaxST extension
- --buflen=ST_BUFLEN
MaxSt buffer length in s
- --corr=ST_CORR
MaxSt subspace correlation
- --trans=MV_TRANS
Transforms the data into the coil definitions of in_fname, or into the default frame
- --movecomp
Estimates and compensates head movements in continuous raw data
- --headpos
Estimates and stores head position parameters, but does not compensate movements
- --hp=MV_HP
Stores head position data in an ascii file
- --hpistep=MV_HPISTEP
Sets head position update interval in ms
- --hpisubt=MV_HPISUBT
Subtracts hpi signals: sine amplitudes, amp + baseline, or switch off
- --nohpicons
Do not check initial consistency isotrak vs hpifit
- --linefreq=LINEFREQ
Sets the basic line interference frequency (50 or 60 Hz)
- --nooverwrite
Do not overwrite output file if it already exists
- --args=MX_ARGS
Additional command line arguments to pass to MaxFilter
Examples#
$ mne maxfilter -i sample_audvis_raw.fif --st
This will apply MaxFilter with the MaxSt extension. The origin used by MaxFilter is computed by mne-python by fitting a sphere to the headshape points.
mne prepare_bem_model#
Create a BEM solution using the linear collocation approach.#
Usage: mne prepare_bem_model [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- --bem=FILE
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.
- --sol=FILE
The name of the resulting file containing BEM solution (geometry matrix). It uses the linear collocation approach. The file should end with -bem-sof.fif.
- --verbose
Enable verbose mode (printing of log messages).
Examples#
$ mne prepare_bem_model --bem sample-5120-5120-5120-bem.fif
mne report#
Create mne report for a folder.#
Usage: mne report [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -p PATH, --path=PATH
Path to folder who MNE-Report must be created
- -i FILE, --info=FILE
File from which info dictionary is to be read
- -c FILE, --cov=FILE
File from which noise covariance is to be read
- --bmin=BMIN
Time at which baseline correction starts for evokeds
- --bmax=BMAX
Time at which baseline correction stops for evokeds
- -d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR
The subjects directory
- -s SUBJECT, --subject=SUBJECT
The subject name
- --no-browser
Do not open MNE-Report in browser
- --overwrite
Overwrite html report if it already exists
- -j N_JOBS, --jobs=N_JOBS
Number of jobs to run in parallel
- -m MRI_DECIM, --mri-decim=MRI_DECIM
Integer factor used to decimate BEM plots
- --image-format=IMAGE_FORMAT
Image format to use (can be ‘png’ or ‘svg’)
- --verbose
Enable verbose mode (printing of log messages).
Examples#
Before getting started with mne report
, make sure the files you want to
render follow the filename conventions defined by MNE:
Data object |
Filename convention (ends with) |
---|---|
raw |
-raw.fif(.gz), -raw_sss.fif(.gz), -raw_tsss.fif(.gz), _meg.fif(.gz), _eeg.fif(.gz), _ieeg.fif(.gz) |
events |
-eve.fif(.gz) |
epochs |
-epo.fif(.gz) |
evoked |
-ave.fif(.gz) |
covariance |
-cov.fif(.gz) |
trans |
-trans.fif(.gz) |
forward |
-fwd.fif(.gz) |
inverse |
-inv.fif(.gz) |
To generate a barebones report from all the *.fif files in the sample dataset, invoke the following command in a system (e.g., Bash) shell:
$ mne report --path MNE-sample-data/ --verbose
On successful creation of the report, it will open the HTML in a new tab in
the browser. To disable this, use the --no-browser
option.
TO generate a report for a single subject, give the SUBJECT
name and
the SUBJECTS_DIR
and this will generate the MRI slices (with BEM
contours overlaid on top if available):
$ mne report --path MNE-sample-data/ --subject sample --subjects-dir \
MNE-sample-data/subjects --verbose
To properly render trans
and covariance
files, add the measurement
information:
$ mne report --path MNE-sample-data/ \
--info MNE-sample-data/MEG/sample/sample_audvis-ave.fif \
--subject sample --subjects-dir MNE-sample-data/subjects --verbose
To render whitened evoked
files with baseline correction, add the noise
covariance file:
$ mne report --path MNE-sample-data/ \
--info MNE-sample-data/MEG/sample/sample_audvis-ave.fif \
--cov MNE-sample-data/MEG/sample/sample_audvis-cov.fif --bmax 0 \
--subject sample --subjects-dir MNE-sample-data/subjects --verbose
To generate the report in parallel:
$ mne report --path MNE-sample-data/ \
--info MNE-sample-data/MEG/sample/sample_audvis-ave.fif \
--subject sample --subjects-dir MNE-sample-data/subjects \
--verbose --jobs 6
For help on all the available options, do:
$ mne report --help
mne setup_forward_model#
Create a BEM model for a subject.#
Usage: mne setup_forward_model [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s SUBJECT, --subject=SUBJECT
Subject name (required)
- --model=MODEL
Output file name. Use a name <dir>/<name>-bem.fif
- --ico=ICO
The surface ico downsampling to use, e.g. 5=20484, 4=5120, 3=1280. If None, no subsampling is applied.
- --brainc=BRAINC
Defines the brain compartment conductivity. The default value is 0.3 S/m.
- --skullc=SKULLC
Defines the skull compartment conductivity. The default value is 0.006 S/m.
- --scalpc=SCALPC
Defines the scalp compartment conductivity. The default value is 0.3 S/m.
- --homog
Use a single compartment model (brain only) instead a three layer one (scalp, skull, and brain). If this flag is specified, the options –skullc and –scalpc are irrelevant.
- -d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR
Subjects directory
- --verbose
Enable verbose mode (printing of log messages).
Examples#
$ mne setup_forward_model -s 'sample'
mne setup_source_space#
Set up bilateral hemisphere surface-based source space with subsampling.#
Usage: mne setup_source_space [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s SUBJECT, --subject=SUBJECT
Subject name (required)
- --src=FILE
Output file name. Use a name <dir>/<name>-src.fif
- --morph=SUBJECT_TO
morph the source space to this subject
- --surf=SURFACE
The surface to use. (default to white)
- --spacing=SPACING
Specifies the approximate grid spacing of the source space in mm. (default to 7mm)
- --ico=ICO
use the recursively subdivided icosahedron to create the source space.
- --oct=OCT
use the recursively subdivided octahedron to create the source space.
- -d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR
Subjects directory
- -n N_JOBS, --n-jobs=N_JOBS
The number of jobs to run in parallel (default 1). Requires the joblib package. Will use at most 2 jobs (one for each hemisphere).
- --add-dist=ADD_DIST
Add distances. Can be “True”, “False”, or “patch” to only compute cortical patch statistics (like the –cps option in MNE-C; requires SciPy >= 1.3)
- -o, --overwrite
to write over existing files
- --verbose
Enable verbose mode (printing of log messages).
Examples#
$ mne setup_source_space --subject sample
.. note : Only one of --ico, --oct or --spacing options can be set at the same
time. Default to oct6.
mne show_fiff#
Show the contents of a FIFF file.#
Usage: mne show_fiff <file>
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -t TAG, --tag=TAG
provide information about this tag
Examples#
$ mne show_fiff test_raw.fif
To see only tag 102:
$ mne show_fiff test_raw.fif --tag=102
mne show_info#
Show measurement info from .fif file.#
Usage: mne show_info <file>
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
Examples#
$ mne show_info sample_audvis_raw.fif
mne surf2bem#
Convert surface to BEM FIF file.#
Usage: mne surf2bem [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s FILE, --surf=FILE
Surface in Freesurfer format
- -f FILE, --fif=FILE
FIF file produced
- -i ID, --id=ID
Surface Id (e.g. 4 for head surface)
Examples#
$ mne surf2bem --surf ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.seghead \
--fif ${SUBJECTS_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif \
--id=4
mne sys_info#
Show system information.#
Usage: mne sys_info
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -p, --show-paths
Show module paths
- -d, --developer
Show additional developer module information
- -a, --ascii
Use ASCII instead of unicode symbols
Examples#
$ mne sys_info
mne watershed_bem#
Create BEM surfaces using the watershed algorithm included with FreeSurfer.#
Usage: mne watershed_bem [options]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s SUBJECT, --subject=SUBJECT
Subject name (required)
- -d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR
Subjects directory
- -o, --overwrite
Write over existing files
- -v VOLUME, --volume=VOLUME
Defaults to T1
- -a, --atlas
Specify the –atlas option for mri_watershed
- -g, --gcaatlas
Specify the –brain_atlas option for mri_watershed
- -p PREFLOOD, --preflood=PREFLOOD
Change the preflood height
- --copy
Use copies instead of symlinks for surfaces
- -t T1, --T1=T1
Whether or not to pass the -T1 flag (can be true, false, 0, or 1). By default it takes the same value as gcaatlas.
- -b BRAINMASK, --brainmask=BRAINMASK
The filename for the brainmask output file relative to the $SUBJECTS_DIR/$SUBJECT/bem/watershed/ directory.
- --verbose
Enable verbose mode (printing of log messages).
Examples#
$ mne watershed_bem -s sample
mne what#
Check type of FIF file.#
Usage: mne what fname [fname2 ...]
Options#
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
Examples#
$ mne what sample_audvis_raw.fif
raw