Fif file conversion/importation

Transcription

1 Fif file conversion/importation Reading of sensors positions Reading of MEG data Reading of anatomical landmark Three-dimensional display of magnetometers vs gradiometers Re-labeling of MEG sensors names with meaningful names G or H for gradiometer (with respect to the orientation) M for magnetometer L (left), Z (median) or R (right) F (frontal), C (central) or O (occipital)

2 Neuromag fif file Correction SSS + Head reference position Maxfilter DataHandler FastTF Fichier txt avec positions Data Editor MUSE Conversion/importation Définition des triggers Détection ondes R sur l ECG Détection des blinks Lecture des données MEG Correction artéfacts ECG Pre-processing datahandler Export des époques Import dans Brainstorm Rejection d artéfacts EOG Correction d artéfacts EOG (basée sur la PCA) Export des époques dans Matlab Filtrage / moyennage Analyse Temp-Fréquence Interfaçage avec MNE, Fieldtrip, EEGlab TF moyen sur régions d intérêt

3 Trigger script #!/bin/tcsh foreach ds ($1) datahandler -r -adm STI101_1 _1 -ch STI101 $ds datahandler -r -adm STI101_2 _x1 -ch STI101 $ds datahandler -r -adm STI101_3 _xx1 -ch STI101 $ds datahandler -r -adm STI101_4 _xxx1 -ch STI101 $ds datahandler -r -adm STI101_5 _xxxx1 -ch STI101 $ds datahandler -r -adm STI101_6 _xxxxx1 -ch STI101 $ds datahandler -r -adm STI101_7 _xxxxxx1 -ch STI101 $ds datahandler -r -adm STI101_8 _xxxxxxx1 -ch STI101 $ds datahandler -r -adm StdX _100x100 -ch STI101 $ds datahandler -r -adm DvtX _100x101 -ch STI101 $ds datahandler -r -adm OmiX _100x111 -ch STI101 $ds datahandler -r -adm StdY _110x100 -ch STI101 $ds datahandler -r -adm DvtY _110x101 -ch STI101 $ds datahandler -r -adm OmiY _110x111 -ch STI101 $ds datahandler -r -adm Omis _101x111 -ch STI101 $ds datahandler -r -adm Aigu _xxx1xxx -ch STI101 $ds datahandler -r -adm Grave _xxx0xxx -ch STI101 $ds

4 Blink detection #!/bin/tcsh # Detection auto clignements avec marqueurs de chaque cote foreach ds ($1) datahandler -r -tm BLINK maxvar -4 blinkdetect -time 0.4 -ch EOG061 $ds Threshold to optimize deping on your recording Select the good EOG channel

5 Filtering/averaging #!/bin/tcsh Time delay trigger/stim foreach ds ($1) foreach cond(stdx StdY DvtX DvtY OmiX OmiY Omis) datahandler -r -sync "((${cond}+.11)[ ] &BLINK[BLINK]~)&BAD[BAD]~" -time lpf 40 -hpf.1 - avg $ds ${cond}_$ds Averaging excepted in periods with artefacts Filtering Averaging period (start time, period duration)

6 Script correction EOG #!/bin/tcsh # Correction clignements (retrait 1ère composante) autour des marqueurs BLINK foreach ds (raw*.ds) # calcul des composantes magnétomètres datahandler -r -pcam2 BLINK 3 -ch_begin "MR ML MZ" $ds datahandler -r -sgf ch PCM01 $ds datahandler -r -rmam2 BLINK -mag -ch "fcm01" $ds -new CorrBlink1_ -r foreach ds (CorrBlink1_*.ds) # calcul des composantes gradiomètres datahandler -r -pcam2 BLINK 3 -ch_begin "GR GL GZ HR HL HZ" $ds datahandler -r -sgf ch QCM01 $ds datahandler -r -rmam2 BLINK -grad -ch "gcm01" $ds -new CorrBlink2_ -r foreach ds (CorrBlink2_*.ds) # calcul des composantes datahandler -r -pcam2 BLINK 3 -eeg $ds datahandler -r -sgf ch PCE01 $ds datahandler -r -rmam2 BLINK -eeg -ch "fce01" $ds -new CorrBlinkDEF_ -r

7 EEG avant correction

8 EEG après correction

9 Magnétomètres avant correction

10 Magnétomètres après correction

11 Gradiomètres avant correction

12 Gradiomètres après correction

13 Script TF #!/bin/tcsh -f mkdir TF foreach subj (tb070020) echo ${subj} ###compute Time frequency transforms for each condition and each subject foreach cond (FreqXX RareXX OmiXX FreqXY RareXY OmiXY OmiExpected) echo ${cond} /neurospin/local/fast_tf-4.5.4/bin/fast_tf --power --z_score\ --first_frequency 6 \ --last_frequency 120 \ --frequency_step 2 \ --blackman_win 0.2\ --wavelet_m 7 \ --output_file TF/${subj}_${cond} \ --marker ${cond} \ --begin_analysis _analysis 1.5 \ --begin_baseline _baseline 0.0 \ --verbose --rewrite \ --fft_parameters_file /tmp/testfftw \ --input_files CorrCardio_*${subj}_090403_run1_sss.ds \ --input_files CorrCardio_*${subj}_090403_run2_sss.ds \ --input_files CorrCardio_*${subj}_090403_run3_sss.ds \ --input_files CorrCardio_*${subj}_090403_run4_sss.ds \ --input_files CorrCardio_*${subj}_090403_run5_sss.ds \ --input_files CorrCardio_*${subj}_090403_run6_sss.ds \ --input_files CorrCardio_*${subj}_090403_run7_sss.ds \. --restore_fft_parameters --store_fft_parameters

14 To sum up All tools are available here Correction based on physiological signals (ECG, EOG) Corrections only applied on artefactual periods Short computation time Possibility to review your data when you want Different possible outputs after pre-processing But integration of behavioral data from e-prime is not yet straightforward (notably, if you did not take care to define one specific trigger by event)