Command line tools using Python¶

Usage: mne browse_raw [options]
Browse raw data.

Options:





--version
show program’s version number and exit

-h, --help
show this help message and exit

--raw=FILE
Input raw FIF file

--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 ORDER, --order=ORDER

 
Order for plotting (‘type’ or ‘original’)

-p PRELOAD, --preload=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

--clipping=CLIPPING

 
Enable trace clipping mode, either ‘clip’ or
‘transparent’

--filterchpi=FILTERCHPI

 
Enable filtering cHPI signals.




You can do for example:

$ mne browse_raw –raw sample_audvis_raw.fif 
–proj sample_audvis_ecg-proj.fif –eve sample_audvis_raw-eve.fif

Usage: mne bti2fiff [options]
Import BTi / 4D MagnesWH3600 data to fif file.

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




example usage: mne bti2fiff –pdf C,rfDC -o my_raw.fif
Note.
1) 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.
2) The informed guess for the 4D name is E31 for the ECG channel and
E63, E63 for the EOG channels. Pleas 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.

Usage: mne clean_eog_ecg [options]
Clean a raw file from EOG and ECG artifacts with PCA (ie SSP).

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




You can do for example:
$ mne clean_eog_ecg -i in_raw.fif -o clean_raw.fif -e -c

Usage: mne compare_fiff <file_a> <file_b>
Compare FIFF files.

Options:





--version
show program’s version number and exit

-h, --help
show this help message and exit




You can do for example:
$ mne compare_fiff test_raw.fif test_raw_sss.fif

Usage: mne compute_proj_ecg [options]
Compute SSP/PCA projections for ECG artifacts.

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 uV (peak to peak amplitude)

--rej-eog=REJ_EOG

 
EOG rejection parameter in uV (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




You can do for example:

$ 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

Usage: mne compute_proj_eog [options]
Compute SSP/PCA projections for EOG artifacts.

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 uV (peak to peak amplitude)

--rej-eog=REJ_EOG

 
EOG rejection parameter in uV (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




You can do for example:

$ mne compute_proj_eog -i sample_audvis_raw.fif 
–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 
–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.

Usage: mne coreg [options]
Open the coregistration GUI.

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”)

--verbose
Turn on verbose mode.




example usage:  $ mne coreg

Usage: mne flash_bem [options]
Create 3-layer BEM model from Flash MRI images.

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




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


Example usage:
$ mne flash_bem –subject sample

Usage: mne freeview_bem_surfaces [options]
View the 3-Layers BEM model using Freeview.

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.




You can do for example:
$ mne freeview_bem_surfaces -s sample

Usage: mne kit2fiff [options]
Import KIT / NYU data to fif file.

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




example usage:  $ mne kit2fiff –input input.sqd –output output.fif
Use without arguments to invoke GUI:  $ mne kt2fiff

Usage: mne make_scalp_surfaces [options]
Create high-resolution head surfaces for coordinate alignment.

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.

-v, --verbose
Print the debug messages.

-d SUBJECTS_DIR, --subjects-dir=SUBJECTS_DIR

 
Subjects directory

-n, --no-decimate

 
Disable medium and sparse decimations (dense only)




example usage: mne make_scalp_surfaces –overwrite –subject sample

Usage: mne maxfilter [options]
Apply MaxFilter.

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




Example usage:
$ 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.

Usage: mne report [options]
Create mne report for a folder.

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

-v, --verbose
run in verbose mode

--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




Example usage
mne report -p MNE-sample-data/ -i MNE-sample-data/MEG/sample/sample_audvis-ave.fif -d MNE-sample-data/subjects/ -s sample

Usage: mne show_fiff <file>
Show the contents of a FIFF file.

Options:





--version
show program’s version number and exit

-h, --help
show this help message and exit




You can do for example:
$ mne show_fiff test_raw.fif

Usage: mne show_info <file>
Show measurement info from .fif file.

Options:





--version
show program’s version number and exit

-h, --help
show this help message and exit




You can do for example:
$ mne show_info sample_audvis_raw.fif

Usage: mne surf2bem [options]
Convert surface to BEM FIF file.

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)




Example usage
mne surf2bem –surf ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.seghead –fif ${SUBJECTS_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif –id=4

Usage: mne watershed_bem [options]
Create BEM surfaces using the watershed algorithm included with FreeSurfer.

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
Use the subcortical atlas

-p PREFLOOD, --preflood=PREFLOOD

 
Change the preflood height

--verbose=VERBOSE

 
If not None, override default verbose level




You can do for example:
$ mne watershed_bem -s sample