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This command will apply Maxfilter including downsampling, Signal Space Separation (SSS), its temporal extension (ST), and movement compensation. | This command will apply Maxfilter including Signal Space Separation (SSS), its temporal extension (ST), and movement compensation. |
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maxfilter -f input_file.fif -o output_file.fif -st -origin 0 0 45 -frame head -autobad on -ds 3 -movecomp -format short -force | maxfilter -f input_file.fif -o output_file.fif -st -origin 0 0 45 -frame head -autobad on -movecomp -format short -force |
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For more information on these and other options, see the [[attachment:Maxfilter_Manual_v2pt2.pdf|Maxfilter 2.2 Manual]]. |
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 }}} |
Maxfilter Version 2.2
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.
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 2-3 steps, with 1-2 outputs: % % 1. SSS with autobad on, to detect bad channels and write out move parameters % 2. tSSS, downsample by factor 4 (250Hz), and trans to first file if multiple runs % 3. trans to default helmet position (if flag below set) (note trans'ing % direct to default space without realigning runs within subject does not % work so well) 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' 'meg14_0111' 'meg14_0113' 'meg14_0117' }; 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 % matlabpool close force CBU_Cluster 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 TransDefaultFlag = 1; %% 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) transfstfile = ''; orig = []; rad=[]; fit=[]; transtr = {}; raw_stem = {}; % Output directory 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_NoSSS',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 to first file (ie, align within subject if multiple runs) tSSSstr = ' -st 10 -corr 0.98'; %'tSSSstr = ''; if mvcomp_fail(g,s,e,r) == 1 compstr = ''; else compstr = sprintf(' -movecomp inter'); end outfile = fullfile(sub_wd,sprintf('%s_trans1st',raw_stem)) if length(runs{e})>1 & r>1 transtr = sprintf(' -trans %s ',transfstfile) else transfstfile = [outfile '.fif']; transtr = ''; end 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 ''Trans 1st...'' >> %s',movfile)); rik_eval(sprintf('!cat %s.log | sed -n ''/Position change/p'' | cut -f 7- -d '' '' >> %s',outfile,movfile)); %% 3. trans to default helmet space (align across subjects) if TransDefaultFlag transdeffile = fullfile(sub_wd,sprintf('%s_trans1stdef',raw_stem)) transtr = sprintf(' -trans default -origin %d %d %d -frame head -force',orig+[0 -13 6]) filestr = sprintf(' -f %s.fif -o %s.fif',outfile,transdeffile); finstr = [maxfstr filestr transtr sprintf(' -v | tee %s.log',outfile)] rik_eval(finstr); rik_eval(sprintf('!echo ''Trans def...'' >> %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 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) transfstfile = ''; orig = []; rad=[]; fit=[]; transtr = {}; raw_stem = {}; % Output directory 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_NoSSS',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 to first file (ie, align within subject if multiple runs) tSSSstr = ' -st 10 -corr 0.98'; %'tSSSstr = ''; if mvcomp_fail(g,s,e,r) == 1 compstr = ''; else compstr = sprintf(' -movecomp inter'); end outfile = fullfile(sub_wd,sprintf('%s_trans1st',raw_stem)) if length(runs{e})>1 & r>1 transtr = sprintf(' -trans %s ',transfstfile) else transfstfile = [outfile '.fif']; transtr = ''; end 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 ''Trans 1st...'' >> %s',movfile)); rik_eval(sprintf('!cat %s.log | sed -n ''/Position change/p'' | cut -f 7- -d '' '' >> %s',outfile,movfile)); %% 3. trans to default helmet space (align across subjects) if TransDefaultFlag transdeffile = fullfile(sub_wd,sprintf('%s_trans1stdef',raw_stem)) transtr = sprintf(' -trans default -origin %d %d %d -frame head -force',orig+[0 -13 6]) filestr = sprintf(' -f %s.fif -o %s.fif',outfile,transdeffile); finstr = [maxfstr filestr transtr sprintf(' -v | tee %s.log',outfile)] if ParType==1 spmd; rik_eval(finstr); end else rik_eval(finstr); end rik_eval(sprintf('!echo ''Trans def...'' >> %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 end if ParType matlabpool close force CBU_Cluster end