maxfilterTestScript.ipy

import numpy as np

#  make empty list for the names of subjects & files
rawList =  !ls *raw.fif
outputTsssList = []
outputTransList = []
headposLog = []
tsss_mcLog = []
transLog = []
bcFileNames = []

print rawList

# make the lists of files and subjects
for i in range(len(rawList)):
    outputTsssList.append(rawList[i][:-8] + '_tsss_mc.fif')
    outputTransList.append(rawList[i][:-8] + '_tsss_mc_trans.fif')
    headposLog.append(rawList[i][:-8] + '_headpos.txt')
    tsss_mcLog.append(rawList[i][:-8] + '_tsss_mc.log')
    transLog.append(rawList[i][:-8] + '_tsss_mc_trans.log')
    bcFileNames.append(rawList[i][:-8] + '_badChans.csv')



for i in range(len(rawList)):
   
    badChannels = np.genfromtxt(bcFileNames[i], delimiter=',', dtype='int')
    print 'Bad channels =', badChannels
    !/neuro/bin/util/maxfilter -f {rawList[i]} -o {outputTsssList[i]} -st 10 -movecomp -hp {headposLog[i]} -bad {badChannels[i]} -v -force | tee {tsss_mcLog[i]}

for i in range(len(rawList)):
    !/neuro/bin/util/maxfilter -f {outputTsssList[i]} -o {outputTransList[i]} -trans default -force -v | tee {transLog[i]}