|
Size: 16806
Comment:
|
Size: 23030
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| '''[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE] ''' ''Authors: Francois Tadel, Elizabeth Bock, Dimitrios Pantazis, Richard Leahy, Sylvain Baillet'' |
''Authors: Francois Tadel, Elizabeth Bock, Dimitrios Pantazis, John Mosher, Richard Leahy, Sylvain Baillet'' |
| Line 11: | Line 9: |
| The most appropriate analysis pipeline for your data depends on the question you are trying to answer. Before defining what are the main steps of your analysis, you should be able to state clearly the question you want to answer with your data. | The most appropriate analysis pipeline for your data depends on the question you are trying to answer. Before defining what are the main steps of your analysis, you should be able to state clearly the question you want to answer with your recordings. |
| Line 19: | Line 17: |
| * Time-frequency maps | * Frequency or time-frequency maps |
| Line 22: | Line 20: |
| * '''Within subject''': Contrast two experimental conditions across trials, for one single subject. | * '''Single subject''': Contrast two experimental conditions across trials, for one single subject. |
| Line 25: | Line 23: |
| * '''Between subjects''': Contrast two experimental conditions across multiple subjects. | * '''Group analysis, within subject''': Contrast two conditions A and B measured for each subject. |
| Line 28: | Line 26: |
| * '''Between groups''': Contrast two groups of subjects for one given experimental condition. * Files A: Subject-level averages for group #1. * Files B: Subject-level averages for group #2. |
* '''Group analysis, between subjects''': Contrast two groups of subjects for one condition. * Files A: Subject-level averages for group #1 (G1). * Files B: Subject-level averages for group #2 (G2). |
| Line 39: | Line 37: |
| * Significance level obtained with '''two-sided''' tests. * Correct effect size: We identify correctly '''where and when''' the conditions are different. |
* Correct detection: Identify correctly '''where and when''' the conditions are different. |
| Line 42: | Line 39: |
| * '''|A - B| = 0''' * Tests the null hypothesis H0:(|A-B|=0) against the alternative hypothesis H1:(|A-B|>0) * Significance level obtained with '''one-sided''' tests. * Correct effect size: We identify correctly '''where and when''' the conditions are different. * No sign: We cannot say which condition is stronger. * '''|A| = |B|''' * Tests the null hypothesis H0:(|A|=|B|) against the alternative hypothesis H1:(|A|<<HTML(≠)>>|B|) * Significance level obtained with '''two-sided''' tests. * Incorrect effect size: Doesn't detect correctly the effects when A and B have opposite signs. * Correct sign: We can identify correctly which condition has a '''stronger response'''. * |x| represents the modulus of the values: * Absolute value for scalar values (recordings, constrained sources, time-frequency maps) * Norm of the three orientations for unconstrained sources. |
* '''Power(A) = Power(B)''' * Tests the null hypothesis H0:(Power(A)=Power(B)) against the alternative hypothesis H1:(Power(A)<<HTML(≠)>>Power(B)) * Incorrect detection: Not sensitive to the cases where A and B have opposite signs. * Meaningful sign: We can identify correctly which condition has a '''stronger response'''. * Power(x) = |x|<<HTML(<SUP>2</SUP>)>>, where |x| represents the modulus of the values: <<BR>> - Absolute value for scalar values (recordings, constrained sources, time-frequency) <<BR>> - Norm of the three orientations for unconstrained sources. * '''Multiple comparisons''': FDR is a good choice for correcting p-values for multiple comparisons. ==== Design considerations ==== * Use within-subject designs whenever possible (i.e. collect two conditions A and B for each subject), then contrast data at the subject level before comparing data between subjects. * Such designs are not only statistically optimal, but also ameliorate the between-subject sign ambiguities as contrasts can be constructed within each subject. |
| Line 71: | Line 65: |
| ==== How many trials to include? ==== * '''Single subject''': Include all the good trials (unless you have a very low number of trials). <<BR>>See the [[http://neuroimage.usc.edu/brainstorm/Tutorials/Averaging#Number_of_trials|averaging tutorial]]. * '''Group analysis''': Use a similar numbers of trials for all the subjects (no need to be strictly equal), reject the subjects for which you have much less good trials. |
|
| Line 73: | Line 71: |
| * Average the epochs across sessions and subjects: OK. | * Average the epochs across acquisition runs: OK. * Average the epochs across subjects: OK. |
| Line 76: | Line 75: |
| * Group averages: Use the same number of trials for all the subjects. === Statistics: Within subject === |
=== Statistics: Single subject === * '''A ='''''' B''': Parametric or non-parametric t-test, '''independent''', two-tailed. === Statistics: Group analysis, within subject === |
| Line 80: | Line 81: |
| * '''Parametric '''or '''non-parametric''' t-test, '''independent''', two-tailed, FDR-corrected. * Use as many trials as possible for A and B: No need to have an equal number of trials. === Statistics: Within subject === * '''A ='''''' B''' * '''First-level statistic''': Average * For each subject, compute the sensor average for conditions A and B. * Use the same number of trials for all the the averages. * '''Second-level statistic''': t-test * '''Parametric''' or '''non-parametric''' t-test, '''paired''', two-tailed, FDR-corrected. === Statistics: Between groups === * '''A ='''''' B''' * '''First-level statistic''': Average * For each subject, compute the sensor average for conditions A and B. * Use the same number of trials for all the the averages. * '''Second-level statistic''': t-test * '''Parametric''' or '''non-parametric''' t-test, '''independent''', two-tailed, FDR-corrected. |
* '''First-level statistic''': For each subject, sensor average for conditions A and B. * '''Second-level statistic''': Parametric or non-parametric t-test, '''paired''', two-tailed. === Statistics: Group analysis, between subjects === * '''G1 ='''''' G2''' * '''First-level statistic''': For each subject, sensor average for the conditions to test. * '''Second-level statistic''': Parametric/non-parametric t-test, '''independent''', two-tailed. |
| Line 101: | Line 91: |
| * Average the epochs within each session: OK. * Averaging across sessions: Not advised because the head of the subject may move between runs. * Averaging across subjects: Strongly discouraged because the shape of the heads vary but the sensors are fixed. One sensor does not correspond to the same brain region for different subjects. |
* Average the epochs within each acquisition runs: OK. * Average across runs: Not advised because the head of the subject may move between runs. * Average across subjects: Strongly discouraged because the shape of the heads vary but the sensors are fixed. One sensor does not correspond to the same brain region for different subjects. |
| Line 105: | Line 95: |
| * Note for Elekta/MaxFilter users: You can align all sessions to a reference session, this will allow direct channel comparisons within-subject. Not recommended across subjects. | * Note for Elekta/MaxFilter users: You can align all acquisition run to a reference run, this will allow direct channel comparisons and averaging across runs. Not recommended across subjects. |
| Line 107: | Line 97: |
| * Group averages: Use the same number of trials for all the sessions. === Statistics: Within subject === * '''A ='''''' B''' * '''Parametric '''or '''non-parametric''' t-test, '''independent''', two-tailed, FDR-corrected. * Use as many trials as possible for A and B: No need to have an equal number of trials. === Statistics: Between subjects === |
=== Statistics: Single subject === * '''A ='''''' B''': Parametric or non-parametric t-test, '''independent''', two-tailed. === Statistics: Group analysis === |
| Line 117: | Line 104: |
| === Statistics: Between-groups === * Not recommended with MEG recordings: do your analysis in source space. |
|
| Line 121: | Line 105: |
| === Average: Within subject === 1. '''Sensor average''': Compute one sensor-level average''' '''per acquisition session and condition. <<BR>>Use the '''same number of trials''' for all the averages. 1. '''Sources''': Estimate sources for each average (constrained or unconstrained, no normalization). |
=== Average: Single subject === 1. '''Sensor average''': Compute one sensor-level average''' '''per acquisition run and per condition. 1. '''Sources''': Estimate sources for each average (constrained, no normalization). 1. '''Source average''': Average the source-level run averages to get one subject average.<<BR>>Compute a weighted average to balance for different numbers of trials across runs. 1. '''Low-pass filter''' your evoked responses (optional). * If you filter the average before normalizing wrt baseline, it will lead to an underestimation of the baseline variance, and therefore to an overestimation of the Z scores computed in the next step, especially if the baseline is too short (typically less than 200 time points). The filter increases the autocorrelation of the time series, and therefore biases the estimation of the signal variance ([[https://en.wikipedia.org/wiki/Unbiased_estimation_of_standard_deviation#Effect_of_autocorrelation_.28serial_correlation.29|Wikipedia]]). * If you low-pass filter the evoked responses, you have to take the possible edge effects due to the filter into account. You can either extract a small time window (process Extract > Extract time), or exclude the beginning of the baseline in the Z-score normalization. 1. '''Normalize '''the subject min-norm averages: Z-score wrt baseline (no absolute value).<<BR>>Justification: The amplitude range of current densities may vary between subjects because of anatomical or experimental differences. This normalization helps bringing the different subjects to the same range of values. 1. '''Do not rectify the cortical maps''', but display them as absolute values if needed. === Average: Group analysis === 1. '''Subject averages''': Compute within-subject averages for all the subjects, as described above. 1. '''Rectify''' the cortical maps (process: Pre-process > Absolute value). <<BR>>Justification: Cortical maps have ambiguous signs across subjects: reconstructed sources depend heavily on the orientation of true cortical sources. Given the folding patterns of individual cortical anatomies vary considerably, cortical maps have subject-specific amplitude and sign ambiguities. This is true even if a standard anatomy is used for reconstruction. 1. '''Project '''the individual source maps on a template (only when using the individual brains). <<BR>> For more details, see tutorial: [[Tutorials/CoregisterSubjects|Group analysis: Subject coregistration]]. 1. '''Group average''': Compute grand averages of all the subjects.<<BR>>Do __not__ use a weighted average: all the subjects should have the same weight in this average. 1. '''Smooth '''spatially the source maps (optional).<<BR>>You can smooth after step #3 for computing non-parametric statistics with the subject averages. For a simple group average, it is equivalent to smooth before of after computing the average. === Difference of averages: Within subject === 1. '''Sensor average''': Compute one sensor-level average per acquisition run and condition. 1. '''Sources''': Estimate sources for each average (constrained, no normalization). |
| Line 125: | Line 127: |
| 1. '''Low-pass filter''' below 40Hz for evoked responses (optional). 1. '''Normalize '''the subject min-norm averages: Z-score vs. baseline (no absolute value).<<BR>>Justification: The amplitude range of current densities may vary between subjects because of anatomical or experimental differences. This normalization helps bringing the different subjects to the same range of values. 1. '''Do not rectify the cortical maps''', but display them in absolute values. === Average: Between subjects === 1. '''Subject averages''': Compute the within-subject averages for all the subjects, as described above. 1. '''Rectify''' the cortical maps (apply an absolute value). <<BR>>Justification: Cortical maps have ambiguous signs across subjects: reconstructed sources depend heavily on the orientation of true cortical sources. Given the folding patterns of individual cortical anatomies vary considerably, cortical maps have subject-specific amplitude and sign ambiguities. This is true even if a standard anatomy is used for reconstruction. 1. '''Project '''the individual source maps on a template (only when using the individual brains). <<BR>> For more details, see tutorial: [[Tutorials/CoregisterSubjects|Group analysis: Subject coregistration]]. 1. '''Smooth '''spatially the sources.<<BR>>Justification: The effects observed with constrained cortical maps may be artificially very focal, not overlapping very well between subjects. Smoothing the cortical maps may help the activated regions overlap between subjects. 1. '''Group average''': Compute grand averages of all the subjects. === Average: Between groups === * Same as average between subjects. |
1. '''Subject difference''': Compute the difference between conditions for each subject #i: (A,,i,,-B,,i,,) 1. '''Low-pass filter''' the difference (optional) 1. '''Normalize '''the difference: Z-score wrt baseline (no absolute value): Z(A,,i,,-B,,i,,) 1. '''Rectify''' the difference (apply an absolute value): |Z(A,,i,,-B,,i,,)| 1. '''Project '''the individual difference on a template (only when using the individual brains). 1. '''Group average''': Compute grand averages of all the subjects: avg(|Z(A,,i,,-B,,i,,)|). 1. '''Smooth '''spatially the source maps (optional). |
| Line 141: | Line 138: |
| 1. '''Subject averages''': Compute the subject averages for conditions A and B, as described above. 1. '''Subject difference''': Compute the difference between conditions for each subject (A-B). 1. '''Rectify''' the difference of source maps (apply an absolute value). 1. '''Project '''the individual difference on a template. 1. '''Smooth '''spatially the sources. 1. '''Group average''': Compute grand averages of all the subjects: average_subjects(|Ai-Bi|). === Difference of averages: Between groups === 1. '''Subject averages''': Compute the subject averages, as described above (rectified values). 1. '''Grand averages''': Compute the group-level averages for groups #1 and #2 as described in "Average: Between subjects" 1. '''Difference''': Compute the difference between group-level averages: avg(|A1|)-avg(|A2|) |
1. '''Grand averages''': Compute averages for groups #1 and #2 as in ''Average:Group analysis.'' 1. '''Difference''': Compute the difference between group-level averages: avg(|G,,1,,|)-avg(|G,,2,,|) |
| Line 154: | Line 143: |
| === Statistics: Within subject === 1. '''Sources''': Compute source maps for each trial (constrained or unconstrained, no normalization) 1. '''Statistics''': Compare all the trials of condition A vs all the trials of condition B.<<BR>>Use as many trials as possible for A and B: No need to have an equal number of trials. 1. '''A = B''' * '''Parametric''' or '''non-parametric''' t-test, '''independent''', two-tailed, FDR-corrected. * Indicates when and where there is a significant effect (but not in which direction). 1. '''|A| = |B|''' * '''Non-parametric''' tests only, '''independent''', two-tailed, FDR-corrected. * Indicates which condition corresponds to a stronger brain response (for a known effect). === Statistics: Between subjects === * '''|A - B| = 0''' * '''Sources''': Compute source maps for each trial (constrained or unconstrained, no normalization) * '''First-level statistic''': Compute a t-statistic for the source maps of all the trials A vs B. * Process2: "Test > Parametric test: Independent": t-test with equal variance * Use as many trials as possible for A and B: No need to have an equal number of trials. * With a relatively high number of trials, the t-values follow approximately a Z-distribution. * '''Second-level statistic''': Compute a one-sampled power test based on the subject t-statistic. * Process1: "Test > Parametric test against zero": One-sampled Chi-square test * This tests for '''|A-B|'''=0 using a power test: X = sum(|ti|^2) ~ Chi-square distribution * '''[TODO]''' This test is not coded yet. * '''|A| = |B|''' * Non-parametric tests, two-tailed, FDR-corrected. === Statistics: Between groups === * '''[TODO]''' === Design considerations === * Use within-subject designs whenever possible (i.e. collect two conditions A and B for each subject), then contrast data within subject before comparing data between subjects. * Such designs are not only statistically optimal, but also ameliorate the between-subject sign ambiguities as contrasts can be constructed within each subject. |
=== Statistics: Single subject === * '''A = B''': Parametric or non-parametric * Compute source maps for each trial (constrained, no normalization). * Parametric or non-parametric two-sample t-test, independent, two-tailed.<<BR>>Identifies correctly '''where and when''' the conditions are different (sign not meaningful). * '''Directionality''': Additional step to know which condition has higher values.<<BR>>Compute the difference of rectified averages: |avg(A,,i,,)|-|avg(B,,i,,)|<<BR>>Combine the significance level (t-test) with the direction (difference): [[http://neuroimage.usc.edu/brainstorm/Tutorials/Statistics#Directionality:_Difference_of_absolute_values|See details]]. * '''|mean(A)| = |mean(B)|''': Non-parametric * Compute source maps for each trial (constrained, no normalization). * Non-parametric independent two-sample "absolute mean test", two-tailed.<<BR>>T = (|mean(A)|-|mean(B)|) / sqrt(|var(A)|/N,,A,, + |var(B)|/N,,B,,) * Interesting alternative that provides at the time a correct estimation of the difference (where and when) and the direction (which condition has higher values). === Statistics: Group analysis, within subject === * '''Power(A-B) = 0''': Parametric * '''First-level statistic''': Rectified difference of normalized averages. <<BR>>Proceed as in ''Difference of averages: Within subjects'', but stop before the group average (after step #8). You obtain one measure '''|A,,i,,-B,,i,,|''' per subject, test these values against zero. * '''Second-level statistic''': Parametric one-sample Chi^2^-test. <<BR>>Power = sum(|A,,i,,-B,,i,,|^2^), i=1..N,,subj,, ~ Chi^2^(N,,subj,,) * Identifies '''where and when''' the conditions are different (sign not meaningful). * Warning: Very sensitive test, with lots of false positive (all the brain can be "significant") * '''|A| = |B|''': Parametric or non-parametric * '''First-level statistic''': Rectified and normalized subject averages. <<BR>>Proceed as in ''Average: Group analysis'' to obtain two averages per subject: A,,i,, and B,,i,,. * '''Second-level statistic''': Parametric or non-parametric two-sample t-test, paired, two-tailed. * This test does not consider the sign difference within a subject, and therefore cannot detect correctly when A and B have opposite signs. Works well and indicates '''which condition has higher values''' when A and B have the same sign within a subject. * '''A = B''': Parametric or non-parametric [anatomy template only] * '''First-level statistic''': Normalized subject averages (not rectified, no projection needed). <<BR>>Proceed as in ''Average: Single subject'' to obtain two averages per subject: A,,i,, and B,,i,,. * '''Second-level statistic''': Parametric or non-parametric two-sample t-test, paired, two-tailed. * Applies only if all the subjects are sharing the same template anatomy. <<BR>>Not recommended when using individual anatomies because of the sign issue between subjects (the signs might be opposed between two subjects, and the projection of non-rectified values to a template might be inaccurate). * '''Power(A) = 0''': Parametric * '''First-level statistic''': Rectified and normalized subject averages. <<BR>>Proceed as in ''Average: Group analysis'' to obtain one average per subject #i: |A,,i,,|. * '''Second-level statistic''': Parametric one-sample Chi^2^-test. <<BR>>PowerA = sum(|A,,i,,|^2^), i=1..N,,subj,, ~ Chi^2^(N,,subj,,). === Statistics: Group analysis, between subjects === * '''|G1| = |G2|''': Non-parametric * '''First-level statistic''': Rectified and normalized subject averages. <<BR>>Proceed as in ''Average: Group analysis'' to obtain one average per subject. * '''Second-level statistic''': Non-parametric two-sample t-test, '''independent''', two-tailed. * '''Power(G1) = Power(G2)''': Parametric * '''First-level statistic''': Rectified and normalized subject averages. <<BR>>Proceed as in ''Average: Group analysis'' to obtain one average per subject: |Ai|. * '''Second-level statistic''': Parametric two-sample power F-test. <<BR>>PowerG1 = sum(A,,i,,^2^), i=1..N,,1,, ~ Chi^2^(N,,1,,)<<BR>>PowerG2 = sum(A,,j,,^2^), j=1..N,,2,, ~ Chi^2^(N,,2,,)<<BR>>F(N,,1,,,N,,2,,) = (PowerG1 / N,,1,,) / (PowerG2 / N,,2,,) |
| Line 187: | Line 183: |
| === Statistics: Within subject === * Three values per vertex. * Use the non-normalized minimum norm maps for all the trials (current density maps, no Z-score). * We need to test the '''norm '''of the three orientations instead of testing the orientations separately. * '''Norm(A) vs. Norm(B)''': * Null hypothesis H0: (|A|=|B|). * '''Non-parametric''' tests only, independent, two-tailed, FDR-corrected. * Incorrect effect size, meaningful sign. === Statistics: Between subjects === * '''(Norm(A-B)=0)''': Non-parametric tests, __'''one-tailed'''__ (non-negative statistic), FDR-corrected. * '''(Norm(A)-Norm(B)=0)''': Non-parametric tests, two-tailed, FDR-corrected. === Statistics: Between groups === [TODO] |
Three values for each grid point, corresponding to the three dipoles orientations (X,Y,Z). <<BR>>We want only one statistic and one p-value per grid point in output. === Averages === * Proceed as indicated above for constrained cortical sources. * Just replace the step '''Rectify''' with '''Flatten''' (process: Sources > Unconstrained to flat map). * The operator |A| has to be interpreted as "norm of the three orientations":<<BR>> |A| = sqrt(A,,x,,^2^ + A,,y,,^2^ + A,,z,,^2^) === Statistics: Single subject === * '''|mean(A)| = |mean(B)|''': Non-parametric * Compute source maps for each trial (unconstrained, no normalization). * Non-parametric independent two-sample "absolute mean test", independent, two-tailed.<<BR>>T = (|mean(A)|-|mean(B)|) / sqrt(|var(A)|/N,,A,, + |var(B)|/N,,B,,) * Provides at the time a correct estimation of the difference (where and when) and the direction (which condition has higher values). === Statistics: Group analysis, within subject === * '''Power(A-B) = 0''': Parametric * '''First-level statistic''': Flattened difference of normalized averages. <<BR>>Proceed as in ''Difference of averages: Within subjects'', but stop before the group average (after step #8). You obtain one measure '''|A,,i,,-B,,i,,|''' per subject, test these values against zero. * '''Second-level statistic''': Parametric one-sample Chi^2^-test for unconstrained sources. <<BR>>Power = sum(|A,,i,,-B,,i,,|^2^), i=1..N,,subj,, ~ Chi^2^(3*N,,subj,,) * Identifies '''where and when''' the conditions are different (sign not meaningful). * Warning: Very sensitive test, with lots of false positive (all the brain can be "significant") * '''|A| = |B|''': Parametric or non-parametric * '''First-level statistic''': Flattened and normalized subject averages. <<BR>>Proceed as in ''Average: Group analysis'' to obtain two averages per subject: A,,i,, and B,,i,,. * '''Second-level statistic''': Parametric or non-parametric two-sample t-test, paired, two-tailed. * This test does not consider the sign difference within a subject, and therefore cannot detect correctly when A and B have opposite signs. Works well and indicates '''which condition has higher values''' when A and B have the same sign within a subject. * '''Power(A) = 0''': Parametric * '''First-level statistic''': Flattened and normalized subject averages. <<BR>>Proceed as in ''Average: Group analysis'' to obtain one average per subject #i: |A,,i,,|. * '''Second-level statistic''': Parametric one-sample Chi^2^-test for unconstrained sources. <<BR>>PowerA = sum(|A,,i,,|^2^) = sum(A,,ix,,^2^+A,,iy,,^2^+A,,iz,,^2^), i=1..N,,subj,, ~ Chi^2^(3*N,,subj,,). === Statistics: Group analysis, between subjects === * '''|G1| = |G2|''': Non-parametric * '''First-level statistic''': Flattened and normalized subject averages. <<BR>>Proceed as in ''Average: Group analysis'' to obtain one average per subject. * '''Second-level statistic''': Non-parametric two-sample t-test, '''independent''', two-tailed. * '''Power(G1) = Power(G2)''': Parametric * '''First-level statistic''': Flattened and normalized subject averages. <<BR>>Proceed as in ''Average: Group analysis'' to obtain one average per subject: |Ai|. * '''Second-level statistic''': Parametric two-sample power F-test (unconstrained sources). <<BR>>PowerG1 = sum(A,,ix,,^2^+A,,iy,,^2^+A,,iz,,^2^), i=1..N,,1,, ~ Chi^2^(3*N,,1,,)<<BR>>PowerG2 = sum(A,,jx,,^2^+A,,jy,,^2^+A,,jz,,^2^), j=1..N,,2,, ~ Chi^2^(3*N,,2,,)<<BR>>F = (PowerG1 / N,,1,,) / (PowerG2 / N,,2,,) ~ F(3*N,,1,,,3*N,,2,,) |
| Line 204: | Line 221: |
| === Statistics: Single subject === | |
| Line 206: | Line 224: |
=== Statistics: Within subject === * Average/constrast cortical maps before summarizing scout activity. |
|
| Line 211: | Line 226: |
| === Statistics: Between subjects === * Comparison of scout time series between subjects is tricky because there is no way to avoid sign ambiguity for different subjects. Thus there are no clear recommendations. Rectifying before comparing scout time series between subjects can be a good idea or not depending on different cases. Having a good understanding of the data (multiple inspections across channels/sources/subjects) can offer hints whether rectifying the scout time series is a good idea. Using unconstrained cortical maps to create the scout time series can ameliorate ambiguity concerns. |
=== Statistics: Group analysis, within subject === * Comparison of scout time series between subjects is tricky because there is no way to avoid sign ambiguity for different subjects. Thus there are no clear recommendations. Rectifying before comparing scout time series between subjects can be a good idea or not depending on different cases. * Having a good understanding of the data (multiple inspections across channels/sources/subjects) can offer hints whether rectifying the scout time series is a good idea. Using unconstrained cortical maps to create the scout time series can ameliorate ambiguity concerns. |
| Line 215: | Line 231: |
| === Statistics: Within subject === * Test the non-normalized time-frequency maps for all the trials (no Z-score or ERS/ERD). * The values tested are power or magnitudes, all positive, so (A=B) and (|A|=|B|) are equivalent. * '''|A| vs |B|''': * Null hypothesis H0: (|A|=|B|) * '''Non-parametric''' tests only, independent, two-tailed, FDR-corrected. === Statistics: Between subjects === * '''(|A|-|B|=0)''': Non-parametric tests, two-tailed, FDR-corrected. === Statistics: Between groups === [TODO] <<TAG(Advanced)>> == Workflow: Current problems [TODO] == The following inconsistencies are still present in the documentation. We are actively working on these issues and will update this tutorial as soon as we found solutions. * [Group analysis] Unconstrained sources: How to compute a Z-score? * Zscore(A): Normalizes each orientation separately, which doesn't make much sense. * Zscore(Norm(A)): Gets rid of the signs, forbids the option of a signed test H0:(Norm(A-B)=0) * See also the tutorial: [[http://neuroimage.usc.edu/brainstorm/Tutorials/SourceEstimation#Z-score|Source estimation]] * We need a way to normalize across the three orientations are the same time. * [Group analysis] Constrained sources: How do we smooth? * Group analysis benefits a lot from smoothing the source maps before computing statistics. * However this requires to apply an absolute value first. How do we do? * [Single subject] Unconstrained sources: How do compare two conditions with multiple trials? * Norm(A)-Norm(B): Cannot detect correctly the differences * (A-B): We test individually each orientation, which doesn't make much sense. * We would need a test for the three orientations at once. * [Group analysis] Rectify source maps? * Recommended in Dimitrios' guidelines, which is incoherent with the rest of the page. |
=== Average: Single subject === * '''Single trials''': Compute time-frequency maps for each trial ('''magnitude''', no normalization).<<BR>>It is a more standard analysis to take the square root of power before a t-test. * '''Subject average''': Average the time-frequency maps together, separately for each condition. This can be done automatically when computing the TF decompositions. * The values are all strictly positive, there is no sign ambiguity: you can directly subtract the averages of the two conditions and interpret the sign of the difference. * If you average time-frequency maps computed on sensor-level data, the same limitations apply as for averaging sensor level data (see sections about MEG and EEG recordings above). === Average: Group analysis === 1. '''Subject averages''': Compute within-subject averages for all the subjects, as described above. 1. '''Normalize''' the subject averages: ERD/ERS or Z-score wrt baseline. 1. '''Group average''': Compute grand averages of all the subjects. 1. '''Difference of averages''': Simply compute the difference of the group averages. === Statistics: Single subject === * '''A = B''': Parametric or non-parametric * Compute time-frequency maps for each trial ('''magnitude''', no normalization). * Parametric or non-parametric two-sample t-test, independent, two-tailed. === Statistics: Group analysis, within subject === * '''A = B''': Parametric or non-parametric [anatomy template only] * '''First-level statistic''': Normalized subject averages (ERS/ERD or Z-score). <<BR>> Proceed as in ''Average: Group analysis'' to obtain two averages per subject: A,,i,, and B,,i,,. * '''Second-level statistic''': Parametric or non-parametric two-sample t-test, paired, two-tailed. === Statistics: Group analysis, between subjects === * '''G1 = G2''': Non-parametric * '''First-level statistic''': Normalized subject averages (ERS/ERD or Z-score). <<BR>> Proceed as in ''Average: Group analysis'' to obtain one average per subject. * '''Second-level statistic''': Parametric or non-parametric two-sample t-test, independent, two-tailed. |
Tutorial 27: Workflows
Authors: Francois Tadel, Elizabeth Bock, Dimitrios Pantazis, John Mosher, Richard Leahy, Sylvain Baillet
This page provides some general recommendations for your event-related analysis. It is not directly related with the auditory dataset, but provides guidelines you should consider for any MEG/EEG experiment.
We do not provide standard analysis pipelines for resting or steady state recordings yet, but we will add a few examples soon in the section Other analysis scenarios of the tutorials page.
Contents
What is your question?
The most appropriate analysis pipeline for your data depends on the question you are trying to answer. Before defining what are the main steps of your analysis, you should be able to state clearly the question you want to answer with your recordings.
What dimension?
- MEG/EEG recordings
- Cortical sources
- Individual anatomy or template
- Constrained (one value per vertex) or unconstrained (three values per grid point)
- Full cortex or regions of interests
- Frequency or time-frequency maps
What kind of experiment?
Single subject: Contrast two experimental conditions across trials, for one single subject.
- Files A: Single trials for condition A.
- Files B: Single trials for condition B.
Group analysis, within subject: Contrast two conditions A and B measured for each subject.
- Files A: Subject-level averages for condition A (all the subjects).
- Files B: Subject-level averages for condition B (all the subjects).
Group analysis, between subjects: Contrast two groups of subjects for one condition.
- Files A: Subject-level averages for group #1 (G1).
- Files B: Subject-level averages for group #2 (G2).
What level of precision?
- Difference of averages
- Statistically significant differences between conditions or groups
What statistical test?
A = B
Tests the null hypothesis H0:(A=B) against the alternative hypothesis H1:(A≠B)
Correct detection: Identify correctly where and when the conditions are different.
- Ambiguous sign: We cannot say which condition is stronger.
Power(A) = Power(B)
Tests the null hypothesis H0:(Power(A)=Power(B)) against the alternative hypothesis H1:(Power(A)≠Power(B))
- Incorrect detection: Not sensitive to the cases where A and B have opposite signs.
Meaningful sign: We can identify correctly which condition has a stronger response.
Power(x) = |x|2, where |x| represents the modulus of the values:
- Absolute value for scalar values (recordings, constrained sources, time-frequency)
- Norm of the three orientations for unconstrained sources.
Multiple comparisons: FDR is a good choice for correcting p-values for multiple comparisons.
Design considerations
- Use within-subject designs whenever possible (i.e. collect two conditions A and B for each subject), then contrast data at the subject level before comparing data between subjects.
- Such designs are not only statistically optimal, but also ameliorate the between-subject sign ambiguities as contrasts can be constructed within each subject.
Common pre-processing pipeline
Most event-related studies can start with the pipeline we've introduced in these tutorials.
- Import the anatomy of the subject (or use a template for all the subjects).
- Access the recordings:
- Link the continuous recordings to the Brainstorm database.
- Prepare the channel file: co-register sensors and MRI, edit type and name of channels.
- Edit the event markers: fix the delays of the triggers, mark additional events.
- Pre-process the signals:
- Evaluate the quality of the recordings with a power spectral density plot (PSD).
- Apply frequency filters (low-pass, high-pass, notch).
- Identify bad channels and bad segments.
- Correct for artifacts with SSP or ICA.
- Import the recordings in the database: epochs around some markers of interest.
How many trials to include?
Single subject: Include all the good trials (unless you have a very low number of trials).
See the averaging tutorial.Group analysis: Use a similar numbers of trials for all the subjects (no need to be strictly equal), reject the subjects for which you have much less good trials.
EEG recordings
Average
- Average the epochs across acquisition runs: OK.
- Average the epochs across subjects: OK.
- Electrodes are in the same standard positions for all the subjects (e.g. 10-20).
- Never use an absolute value for averaging or contrasting sensor-level data.
Statistics: Single subject
A = B: Parametric or non-parametric t-test, independent, two-tailed.
Statistics: Group analysis, within subject
A = B
First-level statistic: For each subject, sensor average for conditions A and B.
Second-level statistic: Parametric or non-parametric t-test, paired, two-tailed.
Statistics: Group analysis, between subjects
G1 = G2
First-level statistic: For each subject, sensor average for the conditions to test.
Second-level statistic: Parametric/non-parametric t-test, independent, two-tailed.
MEG recordings
Average
- Average the epochs within each acquisition runs: OK.
- Average across runs: Not advised because the head of the subject may move between runs.
- Average across subjects: Strongly discouraged because the shape of the heads vary but the sensors are fixed. One sensor does not correspond to the same brain region for different subjects.
- Tolerance for data exploration: Averaging across runs and subjects can be useful for identifying time points and sensors with interesting effects but should be avoided for formal analysis.
- Note for Elekta/MaxFilter users: You can align all acquisition run to a reference run, this will allow direct channel comparisons and averaging across runs. Not recommended across subjects.
- Never use an absolute value for averaging or contrasting sensor-level data.
Statistics: Single subject
A = B: Parametric or non-parametric t-test, independent, two-tailed.
Statistics: Group analysis
- Not recommended with MEG recordings: do your analysis in source space.
Constrained cortical sources
Average: Single subject
Sensor average: Compute one sensor-level average per acquisition run and per condition.
Sources: Estimate sources for each average (constrained, no normalization).
Source average: Average the source-level run averages to get one subject average.
Compute a weighted average to balance for different numbers of trials across runs.Low-pass filter your evoked responses (optional).
If you filter the average before normalizing wrt baseline, it will lead to an underestimation of the baseline variance, and therefore to an overestimation of the Z scores computed in the next step, especially if the baseline is too short (typically less than 200 time points). The filter increases the autocorrelation of the time series, and therefore biases the estimation of the signal variance (Wikipedia).
If you low-pass filter the evoked responses, you have to take the possible edge effects due to the filter into account. You can either extract a small time window (process Extract > Extract time), or exclude the beginning of the baseline in the Z-score normalization.
Normalize the subject min-norm averages: Z-score wrt baseline (no absolute value).
Justification: The amplitude range of current densities may vary between subjects because of anatomical or experimental differences. This normalization helps bringing the different subjects to the same range of values.Do not rectify the cortical maps, but display them as absolute values if needed.
Average: Group analysis
Subject averages: Compute within-subject averages for all the subjects, as described above.
Rectify the cortical maps (process: Pre-process > Absolute value).
Justification: Cortical maps have ambiguous signs across subjects: reconstructed sources depend heavily on the orientation of true cortical sources. Given the folding patterns of individual cortical anatomies vary considerably, cortical maps have subject-specific amplitude and sign ambiguities. This is true even if a standard anatomy is used for reconstruction.Project the individual source maps on a template (only when using the individual brains).
For more details, see tutorial: Group analysis: Subject coregistration.Group average: Compute grand averages of all the subjects.
Do not use a weighted average: all the subjects should have the same weight in this average.Smooth spatially the source maps (optional).
You can smooth after step #3 for computing non-parametric statistics with the subject averages. For a simple group average, it is equivalent to smooth before of after computing the average.
Difference of averages: Within subject
Sensor average: Compute one sensor-level average per acquisition run and condition.
Sources: Estimate sources for each average (constrained, no normalization).
Source average: Average the source-level session averages to get one subject average.
Subject difference: Compute the difference between conditions for each subject #i: (Ai-Bi)
Low-pass filter the difference (optional)
Normalize the difference: Z-score wrt baseline (no absolute value): Z(Ai-Bi)
Rectify the difference (apply an absolute value): |Z(Ai-Bi)|
Project the individual difference on a template (only when using the individual brains).
Group average: Compute grand averages of all the subjects: avg(|Z(Ai-Bi)|).
Smooth spatially the source maps (optional).
Difference of averages: Between subjects
Grand averages: Compute averages for groups #1 and #2 as in Average:Group analysis.
Difference: Compute the difference between group-level averages: avg(|G1|)-avg(|G2|)
Limitations: Because we rectify the source maps before computing the difference, we lose the ability to detect the differences between equal values of opposite signs. And we cannot keep the sign because we are averaging across subjects. Therefore, many effects are not detected correctly.
Statistics: Single subject
A = B: Parametric or non-parametric
- Compute source maps for each trial (constrained, no normalization).
Parametric or non-parametric two-sample t-test, independent, two-tailed.
Identifies correctly where and when the conditions are different (sign not meaningful).Directionality: Additional step to know which condition has higher values.
Compute the difference of rectified averages: |avg(Ai)|-|avg(Bi)|
Combine the significance level (t-test) with the direction (difference): See details.
|mean(A)| = |mean(B)|: Non-parametric
- Compute source maps for each trial (constrained, no normalization).
Non-parametric independent two-sample "absolute mean test", two-tailed.
T = (|mean(A)|-|mean(B)|) / sqrt(|var(A)|/NA + |var(B)|/NB)- Interesting alternative that provides at the time a correct estimation of the difference (where and when) and the direction (which condition has higher values).
Statistics: Group analysis, within subject
Power(A-B) = 0: Parametric
First-level statistic: Rectified difference of normalized averages.
Proceed as in Difference of averages: Within subjects, but stop before the group average (after step #8). You obtain one measure |Ai-Bi| per subject, test these values against zero.Second-level statistic: Parametric one-sample Chi2-test.
Power = sum(|Ai-Bi|2), i=1..Nsubj ~ Chi2(Nsubj)Identifies where and when the conditions are different (sign not meaningful).
- Warning: Very sensitive test, with lots of false positive (all the brain can be "significant")
|A| = |B|: Parametric or non-parametric
First-level statistic: Rectified and normalized subject averages.
Proceed as in Average: Group analysis to obtain two averages per subject: Ai and Bi.Second-level statistic: Parametric or non-parametric two-sample t-test, paired, two-tailed.
This test does not consider the sign difference within a subject, and therefore cannot detect correctly when A and B have opposite signs. Works well and indicates which condition has higher values when A and B have the same sign within a subject.
A = B: Parametric or non-parametric [anatomy template only]
First-level statistic: Normalized subject averages (not rectified, no projection needed).
Proceed as in Average: Single subject to obtain two averages per subject: Ai and Bi.Second-level statistic: Parametric or non-parametric two-sample t-test, paired, two-tailed.
Applies only if all the subjects are sharing the same template anatomy.
Not recommended when using individual anatomies because of the sign issue between subjects (the signs might be opposed between two subjects, and the projection of non-rectified values to a template might be inaccurate).
Power(A) = 0: Parametric
First-level statistic: Rectified and normalized subject averages.
Proceed as in Average: Group analysis to obtain one average per subject #i: |Ai|.Second-level statistic: Parametric one-sample Chi2-test.
PowerA = sum(|Ai|2), i=1..Nsubj ~ Chi2(Nsubj).
Statistics: Group analysis, between subjects
|G1| = |G2|: Non-parametric
First-level statistic: Rectified and normalized subject averages.
Proceed as in Average: Group analysis to obtain one average per subject.Second-level statistic: Non-parametric two-sample t-test, independent, two-tailed.
Power(G1) = Power(G2): Parametric
First-level statistic: Rectified and normalized subject averages.
Proceed as in Average: Group analysis to obtain one average per subject: |Ai|.Second-level statistic: Parametric two-sample power F-test.
PowerG1 = sum(Ai2), i=1..N1 ~ Chi2(N1)
PowerG2 = sum(Aj2), j=1..N2 ~ Chi2(N2)
F(N1,N2) = (PowerG1 / N1) / (PowerG2 / N2)
Unconstrained cortical sources
Three values for each grid point, corresponding to the three dipoles orientations (X,Y,Z).
We want only one statistic and one p-value per grid point in output.
Averages
- Proceed as indicated above for constrained cortical sources.
Just replace the step Rectify with Flatten (process: Sources > Unconstrained to flat map).
The operator |A| has to be interpreted as "norm of the three orientations":
|A| = sqrt(Ax2 + Ay2 + Az2)
Statistics: Single subject
|mean(A)| = |mean(B)|: Non-parametric
- Compute source maps for each trial (unconstrained, no normalization).
Non-parametric independent two-sample "absolute mean test", independent, two-tailed.
T = (|mean(A)|-|mean(B)|) / sqrt(|var(A)|/NA + |var(B)|/NB)- Provides at the time a correct estimation of the difference (where and when) and the direction (which condition has higher values).
Statistics: Group analysis, within subject
Power(A-B) = 0: Parametric
First-level statistic: Flattened difference of normalized averages.
Proceed as in Difference of averages: Within subjects, but stop before the group average (after step #8). You obtain one measure |Ai-Bi| per subject, test these values against zero.Second-level statistic: Parametric one-sample Chi2-test for unconstrained sources.
Power = sum(|Ai-Bi|2), i=1..Nsubj ~ Chi2(3*Nsubj)Identifies where and when the conditions are different (sign not meaningful).
- Warning: Very sensitive test, with lots of false positive (all the brain can be "significant")
|A| = |B|: Parametric or non-parametric
First-level statistic: Flattened and normalized subject averages.
Proceed as in Average: Group analysis to obtain two averages per subject: Ai and Bi.Second-level statistic: Parametric or non-parametric two-sample t-test, paired, two-tailed.
This test does not consider the sign difference within a subject, and therefore cannot detect correctly when A and B have opposite signs. Works well and indicates which condition has higher values when A and B have the same sign within a subject.
Power(A) = 0: Parametric
First-level statistic: Flattened and normalized subject averages.
Proceed as in Average: Group analysis to obtain one average per subject #i: |Ai|.Second-level statistic: Parametric one-sample Chi2-test for unconstrained sources.
PowerA = sum(|Ai|2) = sum(Aix2+Aiy2+Aiz2), i=1..Nsubj ~ Chi2(3*Nsubj).
Statistics: Group analysis, between subjects
|G1| = |G2|: Non-parametric
First-level statistic: Flattened and normalized subject averages.
Proceed as in Average: Group analysis to obtain one average per subject.Second-level statistic: Non-parametric two-sample t-test, independent, two-tailed.
Power(G1) = Power(G2): Parametric
First-level statistic: Flattened and normalized subject averages.
Proceed as in Average: Group analysis to obtain one average per subject: |Ai|.Second-level statistic: Parametric two-sample power F-test (unconstrained sources).
PowerG1 = sum(Aix2+Aiy2+Aiz2), i=1..N1 ~ Chi2(3*N1)
PowerG2 = sum(Ajx2+Ajy2+Ajz2), j=1..N2 ~ Chi2(3*N2)
F = (PowerG1 / N1) / (PowerG2 / N2) ~ F(3*N1,3*N2)
Regions of interest (scouts)
Statistics: Single subject
- Even within-subject cortical maps have sign ambiguities. MEG has limited spatial resolution and sources in opposing sulcal/gyral areas are reconstructed with inverted signs (constrained orientations only). Averaging activity in cortical regions of interest (scouts) would thus lead to signal cancelation. To avoid this brainstorm uses algorithms to manipulate the sign of individual sources before averaging within a cortical region. Unfortunately, this introduces an amplitude and sign ambiguity in the time course when summarizing scout activity.
As a result, perform any interesting within-subject average/contrast before computing an average scout time series.
- Then consider as constrained or unconstrained source maps.
Statistics: Group analysis, within subject
- Comparison of scout time series between subjects is tricky because there is no way to avoid sign ambiguity for different subjects. Thus there are no clear recommendations. Rectifying before comparing scout time series between subjects can be a good idea or not depending on different cases.
- Having a good understanding of the data (multiple inspections across channels/sources/subjects) can offer hints whether rectifying the scout time series is a good idea. Using unconstrained cortical maps to create the scout time series can ameliorate ambiguity concerns.
Time-frequency maps
Average: Single subject
Single trials: Compute time-frequency maps for each trial (magnitude, no normalization).
It is a more standard analysis to take the square root of power before a t-test.Subject average: Average the time-frequency maps together, separately for each condition. This can be done automatically when computing the TF decompositions.
- The values are all strictly positive, there is no sign ambiguity: you can directly subtract the averages of the two conditions and interpret the sign of the difference.
- If you average time-frequency maps computed on sensor-level data, the same limitations apply as for averaging sensor level data (see sections about MEG and EEG recordings above).
Average: Group analysis
Subject averages: Compute within-subject averages for all the subjects, as described above.
Normalize the subject averages: ERD/ERS or Z-score wrt baseline.
Group average: Compute grand averages of all the subjects.
Difference of averages: Simply compute the difference of the group averages.
Statistics: Single subject
A = B: Parametric or non-parametric
Compute time-frequency maps for each trial (magnitude, no normalization).
- Parametric or non-parametric two-sample t-test, independent, two-tailed.
Statistics: Group analysis, within subject
A = B: Parametric or non-parametric [anatomy template only]
First-level statistic: Normalized subject averages (ERS/ERD or Z-score).
Proceed as in Average: Group analysis to obtain two averages per subject: Ai and Bi.Second-level statistic: Parametric or non-parametric two-sample t-test, paired, two-tailed.
Statistics: Group analysis, between subjects
G1 = G2: Non-parametric
First-level statistic: Normalized subject averages (ERS/ERD or Z-score).
Proceed as in Average: Group analysis to obtain one average per subject.Second-level statistic: Parametric or non-parametric two-sample t-test, independent, two-tailed.