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Maxfilter Version 2.2
Look here for a brief introduction and literature about Maxfilter and its main feature, the Signal Space Separation method.
Example
Version 2.2. is currently the default on our 64-bit machines (see below for more details).
This command will apply Maxfilter including Signal Space Separation (SSS), its temporal extension (ST), and movement compensation.
maxfilter -f input_file.fif -o output_file.fif -st -origin 0 0 45 -frame head -autobad on -movecomp -format short -force
For more information on these and other options, see the Maxfilter 2.2 Manual.
Known problems and bugs
Maxfilter 2.2. cannot do downsampling and filtering at the same time as movement compensation. You will therefore have to run those in a separate step, e.g.
maxfilter -f input_file.fif -o output_file.fif -ds 4 -lpfilt 40
Diagnostics
You can get information about movement parameters using these scripts to analyse maxfilter output.
How to run Maxfilter at the CBSU
Via the CBU load balancing scripts
maxfilter - defaults to running version 2.2 on l43-l59
maxfilter-2.0 - runs version 2.0 on l24-l42
maxfilter-2.1 - runs v 2.1 on l43-l59
maxfilter-2.2 - runs v 2.2 on l43-l59
maxfilter_gui – runs using maxfilter-2.2 on l43-l59
To run without loadbalancing (i.e. on the current machine)
/neuro/bin/util/maxfilter – will run the default version of maxfilter for that machine (v2.0 on l24-42, v2.2 on l43-59)
The higher numbered machines also have the commands:
/neuro/bin/util/maxfilter-2.1
/neuro/bin/util/maxfilter-2.2
Running maxfilter this way does have the potential pitfall that the command /neuro/bin/util/maxfilter will run different versions depending on which machine you’re on.
By calling the actual binary files
/neuro/bin/util/<machine architecture>/maxfilter
/neuro/bin/util/<machine architecture>/maxfilter-2.1
/neuro/bin/util/<machine architecture>/maxfilter-2.2
Example Matlab Script
Courtesy of Rik Henson
% Maxfilter 2.2 Matlab script for AD project (R Henson Jan 2013)
%
% This version has three options for running on our Compute machines, based
% on setting of ParType variable below: 0 = run on Login in serial; 1 = run
% one Compute core (using spmd); 2 = run on multiple Compute cores
% (using parfor) - with one core per subject (though could switch parfor
% loop across experiments if running one subject (NB: cannot parfor across
% runs, because they depend on same origin fitting)
%
% Note that have turned off "movecomp" option via "mvcomp_fail" matrix, because
% this caused apparent random MF2.2 crashes for the pilot subject. Could
% set to 0 for next subject, in case specific to pilot.
%
% This version does just 2 steps, but only one output:
%
% 1. trans with autobad on, to detect bad channels and write out move parameters
% 2. tSSSS, trans default, downsample by factor 4 (250Hz)
clear % May not want/need to!
dat_wd = '/megdata/cbu/multi_oc';
bas_wd = '/imaging/rh01/Projects/AD_MCI/MEG'; % <-- change to yours
groups = {
'Pilots'
'OC1' % Old controls who did scene-object location task
'OC2' % Old controls who did object-quadrant task
};
cbu_codes{1} = {
'meg13_0515' % Pilot1 = Alex; some session names below may not apply)
'meg14_0003' % a young control
};
cbu_codes{2} = {
'meg14_0008'
'meg14_0010'
'meg14_0014'
'meg14_0018'
% 'meg14_0024' % Two runs of this subject don't maxfilter because of HPI problems (so handled by "badrun" variable below)
'meg14_0028'
'meg14_108'
};
cbu_codes{3} = { % Object-quadrant task
'meg14_0031' % Becki wonders about this one?
'meg14_0032'
'meg14_0037'
'meg14_0043'
'meg14_0045'
};
% Experiments
expts = {'object';'scene';'restclosed'; % 'restopen'
};
% Run labels per experiment (not actually needed with new filenames from Pilot2 onwards)
runs{1} = {'_1'; '_2'};
%runs{2} = {'_3' '_4'}; % This was only Pilot1
runs{2} = {'_1'; '_2'};
runs{3} = {''};
%trans_run = [2 2 1]; % Which run WITHIN an experiment to trans too (1 for rest if only one rest run)
%trans_run = [0 0 0]; % If want to skip this step, eg trans default only
%% Bad runs:
badrun = zeros(5,50,3,2); % Assume all runs ok, unless indicated next
subid = find(strcmp(cbu_codes{2},'meg14_0024'));
badrun(2,subid,1,2) = 1; % meg14_0024, object, run 2 cannot be maxfiltered "The origin is only 4 cm from nearest coil!"
badrun(2,subid,2,1) = 1; % meg14_0024, scene, run 1 cannot be maxfiltered "The origin is only 4 cm from nearest coil!"
% Set up directory structures (only needs to be done once)
for e=1:length(expts)
eval(sprintf('!mkdir %s',fullfile(bas_wd,expts{e})));
for g=1:length(groups)
eval(sprintf('!mkdir %s',fullfile(bas_wd,expts{e},groups{g})));
for s = 1:length(cbu_codes{g})
% eval(sprintf('!mkdir %s',fullfile(bas_wd,expts{e},groups{g},sprintf('Sub%02d',s))));
eval(sprintf('!mkdir %s',fullfile(bas_wd,expts{e},groups{g},cbu_codes{g}{s})));
end
end
end
% Any use bad channels? (This option not implemented yet)
% user_bad{1}{3} = [1218 1278];
basestr = ' -ctc /neuro/databases/ctc/ct_sparse.fif -cal /neuro/databases/sss/sss_cal.dat';
basestr = [basestr ' -linefreq 50 -hpisubt amp'];
basestr = [basestr ' -force'];
maxfstr = '!/neuro/bin/util/x86_64-pc-linux-gnu/maxfilter-2.2 '
addpath /imaging/local/meg_misc
addpath /neuro/meg_pd_1.2/
% files where MF2.2 fails when mvcomp included (for some reason) - so turned off below
%mvcomp_fail = zeros(5,50,3,2);
%mvcomp_fail(1,1,1,2) = 1; % Pilot1 object second run
%mvcomp_fail(1,1,2,2) = 1; % Pilot1 scene second run
mvcomp_fail = ones(5,50,3,2); % Turn off all mvcomp, since seems to fail randomly!
movfile = 'trans_move.txt'; % This file will record translations between runs
%ParType = 0; % Fun on Login machines (not generally advised!)
%ParType = 1; % Run maxfilter call on Compute machines using spmd (faster)
ParType = 2; % Run on multiple Compute machines using parfar (best, but less feedback if crashes)
%% open matlabpool if required
if ParType
if matlabpool('size')==0;
MaxNsubs = 1;
if ParType == 2
for g=1:length(cbu_codes)
MaxNsubs = max([MaxNsubs length(cbu_codes{g})]);
end
end
P = cbupool(MaxNsubs);
matlabpool(P)
end
end
%% Main loop (can comment/uncomment lines below if want to parallelise over expts rather than subjects)
for g = 1:length(groups)
fprintf('\n\n%s\n\n',groups{g})
if ParType == 2 % parfor loop
parfor s = 1:length(cbu_codes{g})
raw_wd = dir(fullfile(dat_wd,cbu_codes{g}{s},'1*')); % Just to get date directory (assuming between 20*1*0 and 20*1*9Q!)
raw_wd = raw_wd.name;
parfor e = 1:length(expts) % If doing a single subject (note: cannot embed parfor loops unfortunately)
% for e = 1:length(expts) % If doing a single subject (note: cannot embed parfor loops unfortunately)
orig = []; rad=[]; fit=[]; transtr = {}; raw_stem = {};
% Output directory
% sub_wd = fullfile(bas_wd,expts{e},groups{g},sprintf('Sub%02d',s)), cd(sub_wd)
sub_wd = fullfile(bas_wd,expts{e},groups{g},cbu_codes{g}{s}), cd(sub_wd)
%try eval(sprintf('!mkdir %s',sub_wd)); end % Try not allowed n parfor, so make directories in advance above
rik_eval(sprintf('!touch %s',movfile));
for r = 1:length(runs{e})
raw_file = dir(fullfile(dat_wd,cbu_codes{g}{s},raw_wd,sprintf('%s*%s_raw*',expts{e},runs{e}{r}))); % Get raw FIF file
if isempty(raw_file)
error('Could not find run %d for grp %s, sub %s, exp %s',r,groups{g},cbu_codes{g}{s},expts{e})
else
raw_stem = raw_file.name(1:(end-4));
raw_file = fullfile(dat_wd,cbu_codes{g}{s},raw_wd,raw_file.name);
end
if badrun(g,s,e,r) % Care: need to note that this run not trans'ed (despite name), not sss, etc
outfile = fullfile(sub_wd,sprintf('%s_transdef',raw_stem));
filestr = sprintf(' -f %s -o %s.fif',raw_file,outfile);
finstr = [maxfstr filestr ' -nosss -ds 4' sprintf(' -v | tee %s.log',outfile)];
rik_eval(finstr);
%rik_eval(sprintf('!cp %s %s',raw_file,outfile));
else
%% Fit sphere (since better than MaxFilter does)
if r == 1 % fit sphere doesn't change with run!
incEEG = 0;
if exist(fullfile(sub_wd,'fittmp.txt')); delete(fullfile(sub_wd,'fittmp.txt')); end
if exist(fullfile(sub_wd,sprintf('run_%02d_hpi.txt',r))); delete(fullfile(sub_wd,sprintf('run_%02d_hpi.txt',r))); end
[orig,rad,fit] = meg_fit_sphere(raw_file,sub_wd,sprintf('%s_hpi.txt',raw_stem),incEEG);
delete(fullfile(sub_wd,'fittmp.txt'));
end
origstr = sprintf(' -origin %d %d %d -frame head',orig(1),orig(2),orig(3))
badstr = sprintf(' -autobad %d -badlimit %d',900,7); % 900s is 15mins - ie enough for whole recording!
%% 1. Bad channel detection (this email says important if doing tSSS later https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=NEUROMEG;d3f363f3.1205)
outfile = fullfile(sub_wd,sprintf('%s_bad',raw_stem));
filestr = sprintf(' -f %s -o %s.fif',raw_file,outfile);
% Write out movements too...
posfile = fullfile(sub_wd,sprintf('%s_headpos.txt',raw_stem));
compstr = sprintf(' -headpos -hpistep 10 -hp %s',posfile);
finstr = [maxfstr filestr origstr basestr badstr compstr sprintf(' -v | tee %s.log',outfile)]
rik_eval(finstr);
delete(sprintf('%s.fif',outfile));
% Pull out bad channels from logfile:
badfile = sprintf('%s.txt',outfile); delete(badfile);
rik_eval(sprintf('!cat %s.log | sed -n -e ''/Detected/p'' -e ''/Static/p'' | cut -f 5- -d '' '' > %s',outfile,badfile));
tmp=dlmread(badfile,' '); Nbuf = size(tmp,1);
tmp=reshape(tmp,1,prod(size(tmp)));
tmp=tmp(tmp>0); % Omit zeros (padded by dlmread):
% Get frequencies (number of buffers in which chan was bad):
[frq,allbad] = hist(tmp,unique(tmp));
% Mark bad based on threshold (currently ~5% of buffers (assuming 500 buffers)):
badchans = allbad(frq>0.05*Nbuf);
if isempty(badchans)
badstr = '';
else
badstr = sprintf(' -bad %s',num2str(badchans))
end
%% 2. tSSS and trans (either across runs or default, depending on what commented below)
tSSSstr = ' -st 10 -corr 0.98'; %'tSSSstr = '';
% posfile = fullfile(sub_wd,sprintf('%s_headpos.txt',raw_stem));
if mvcomp_fail(g,s,e,r) == 1
% compstr = sprintf(' -headpos -hpistep 10 -hp %s',posfile); % no headpos file output if no -movecomp?
compstr = '';
else
% compstr = sprintf(' -movecomp inter -hpistep 10 -hp %s',posfile);
compstr = sprintf(' -movecomp inter');
end
outfile = fullfile(sub_wd,sprintf('%s_transdef',raw_stem));
transtr = sprintf(' -trans default -origin %d %d %d -frame head -force',orig+[0 -13 6]);
dsstr = ' -ds 4'; % downsample to 250Hz
filestr = sprintf(' -f %s -o %s.fif',raw_file,outfile);
finstr = [maxfstr filestr basestr badstr tSSSstr compstr origstr transtr dsstr sprintf(' -v | tee %s.log',outfile)]
rik_eval(finstr);
rik_eval(sprintf('!echo ''Transd...'' >> %s',movfile));
rik_eval(sprintf('!cat %s.log | sed -n ''/Position change/p'' | cut -f 7- -d '' '' >> %s',outfile,movfile));
end
end
end
end
else %% non parfor...
for s = 1:length(cbu_codes{g})
raw_wd = dir(fullfile(dat_wd,cbu_codes{g}{s},'1*')); % Just to get date directory (assuming between 20*1*0 and 20*1*9Q!)
raw_wd = raw_wd.name;
for e = 1:length(expts)
orig = []; rad=[]; fit=[]; transtr = {}; raw_stem = {};
% Output directory
% sub_wd = fullfile(bas_wd,expts{e},groups{g},sprintf('Sub%02d',s)), cd(sub_wd)
sub_wd = fullfile(bas_wd,expts{e},groups{g},cbu_codes{g}{s}), cd(sub_wd)
%try eval(sprintf('!mkdir %s',sub_wd)); end % Try not allowed n parfor, so make directories in advance above
rik_eval(sprintf('!touch %s',movfile));
for r = 1:length(runs{e})
raw_file = dir(fullfile(dat_wd,cbu_codes{g}{s},raw_wd,sprintf('%s*%s_raw*',expts{e},runs{e}{r}))); % Get raw FIF file
if isempty(raw_file)
error('Could not find run %d for grp %s, sub %s, exp %s',r,groups{g},cbu_codes{g}{s},expts{e})
else
raw_stem = raw_file.name(1:(end-4));
raw_file = fullfile(dat_wd,cbu_codes{g}{s},raw_wd,raw_file.name);
end
if badrun(g,s,e,r) % Care: need to note that this run not trans'ed (despite name), not sss, etc
outfile = fullfile(sub_wd,sprintf('%s_transdef',raw_stem));
filestr = sprintf(' -f %s -o %s.fif',raw_file,outfile);
finstr = [maxfstr filestr ' -nosss -ds 4' sprintf(' -v | tee %s.log',outfile)];
rik_eval(finstr);
%rik_eval(sprintf('!cp %s %s',raw_file,outfile));
else
%% Fit sphere (since better than MaxFilter does)
if r == 1 % fit sphere doesn't change with run!
incEEG = 0;
if exist(fullfile(sub_wd,'fittmp.txt')); delete(fullfile(sub_wd,'fittmp.txt')); end
if exist(fullfile(sub_wd,sprintf('run_%02d_hpi.txt',r))); delete(fullfile(sub_wd,sprintf('run_%02d_hpi.txt',r))); end
[orig,rad,fit] = meg_fit_sphere(raw_file,sub_wd,sprintf('%s_hpi.txt',raw_stem),incEEG);
delete(fullfile(sub_wd,'fittmp.txt'));
end
origstr = sprintf(' -origin %d %d %d -frame head',orig(1),orig(2),orig(3))
badstr = sprintf(' -autobad %d -badlimit %d',900,7); % 900s is 15mins - ie enough for whole recording!
%% 1. Bad channel detection (this email says important if doing tSSS later https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=NEUROMEG;d3f363f3.1205)
outfile = fullfile(sub_wd,sprintf('%s_bad',raw_stem));
filestr = sprintf(' -f %s -o %s.fif',raw_file,outfile);
% Write out movements too...
posfile = fullfile(sub_wd,sprintf('%s_headpos.txt',raw_stem));
compstr = sprintf(' -headpos -hpistep 10 -hp %s',posfile);
finstr = [maxfstr filestr origstr basestr badstr compstr sprintf(' -v | tee %s.log',outfile)]
if ParType==1
spmd; rik_eval(finstr); end
else
rik_eval(finstr);
end
delete(sprintf('%s.fif',outfile));
% Pull out bad channels from logfile:
badfile = sprintf('%s.txt',outfile); delete(badfile);
rik_eval(sprintf('!cat %s.log | sed -n -e ''/Detected/p'' -e ''/Static/p'' | cut -f 5- -d '' '' > %s',outfile,badfile));
tmp=dlmread(badfile,' '); Nbuf = size(tmp,1);
tmp=reshape(tmp,1,prod(size(tmp)));
tmp=tmp(tmp>0); % Omit zeros (padded by dlmread):
% Get frequencies (number of buffers in which chan was bad):
[frq,allbad] = hist(tmp,unique(tmp));
% Mark bad based on threshold (currently ~5% of buffers (assuming 500 buffers)):
badchans = allbad(frq>0.05*Nbuf);
if isempty(badchans)
badstr = '';
else
badstr = sprintf(' -bad %s',num2str(badchans))
end
%% 2. tSSS and trans (either across runs or default, depending on what commented below)
tSSSstr = ' -st 10 -corr 0.98'; %'tSSSstr = '';
% posfile = fullfile(sub_wd,sprintf('%s_headpos.txt',raw_stem));
if mvcomp_fail(g,s,e,r) == 1
% compstr = sprintf(' -headpos -hpistep 10 -hp %s',posfile); % no headpos file output if no -movecomp?
compstr = '';
else
% compstr = sprintf(' -movecomp inter -hpistep 10 -hp %s',posfile);
compstr = sprintf(' -movecomp inter');
end
outfile = fullfile(sub_wd,sprintf('%s_transdef',raw_stem));
transtr = sprintf(' -trans default -origin %d %d %d -frame head -force',orig+[0 -13 6]);
dsstr = ' -ds 4'; % downsample to 250Hz
filestr = sprintf(' -f %s -o %s.fif',raw_file,outfile);
finstr = [maxfstr filestr basestr badstr tSSSstr compstr origstr transtr dsstr sprintf(' -v | tee %s.log',outfile)]
if ParType==1
spmd; rik_eval(finstr); end
else
rik_eval(finstr);
end
rik_eval(sprintf('!echo ''Transd...'' >> %s',movfile));
rik_eval(sprintf('!cat %s.log | sed -n ''/Position change/p'' | cut -f 7- -d '' '' >> %s',outfile,movfile));
end
end
end
end
end
end
if ParType
matlabpool close
end