Command line tools using Python¶

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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
--eve=FILE: Events file
-d DURATION, --duration=DURATION: Time window for plotting (sec)
-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).

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" \
                       --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 \
                       --l-freq 1 --h-freq 35 \
                       --rej-grad 3000 --rej-mag 4000 --rej-eeg 100

$ mne compute_proj_eog -i sample_audvis_raw.fif \
                       --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”)
--project-eeg: Project EEG electrodes to the head surface (for visualization purposes only)
--orient-to-surface: Orient points to the surface.
--scale-by-distance: Scale points by distance from the surface.
--mark-inside: Mark points inside the head using a different color.
--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, --noflash30: Skip the 30-degree flip angle data
-n, --noconvert: 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: The directory containing flash05.mgz and flash30.mgz files (defaults to $SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps

Examples¶

$ mne flash_bem --subject=sample

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 are inputted in DICOM format. 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.

Before running this script do the following: (unless the –noconvert option is specified)

Copy all of your FLASH images in a single directory <source> and create a directory <dest> to hold the output of mne_organize_dicom
cd to <dest> and run $ mne_organize_dicom <source> to create an appropriate directory structure
Create symbolic links to make flash05 and flash30 point to the appropriate series: $ ln -s <FLASH 5 series dir> flash05 $ ln -s <FLASH 30 series dir> flash30 Some partition formats (e.g. FAT32) do not support symbolic links. In this case, copy the file to the appropriate series: $ cp <FLASH 5 series dir> flash05 $ cp <FLASH 30 series dir> flash30
cd to the directory where flash05 and flash30 links are
Set SUBJECTS_DIR and SUBJECT environment variables appropriately
Run this script

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
-f, --force: Force transformation of surface into bem.
-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 sec, e.g.: 0 30 120 150
--force: Ignore program warnings
--st: Apply the time-domain MaxST extension
--buflen=ST_BUFLEN: MaxSt buffer length in sec
--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
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 sur 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

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