Projecting Sources Error

[Sean_Carruthers]

Brainstorm,

Im projecting the computed sources of one subject onto a Default brain that includes a FreeSurfer Atlas created from all subjects.

My procedure goes like this:

Compute Head Model - overlapping Spheres
Compute Noise Covariance
Compute Sources
Average the sources from all trials
Project Averaged Source file onto the Default anatomy w/ FS atlas.

I have previously done this with the same data set, same participant.
however today im getting this promt

** Error: Line 236: Index exceeds matrix dimensions.
**
** Call stack:
** >bst_project_sources.m at 236
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@bst_project_sources,ResultFiles,sDefCortex(iCort).FileName) at 1995***

I run the same procedure on a different participant and works.
Its just one participant who with the same data set, the above procedure worked.
Ive deleted their subject and re-started from scratch (e.g., import FS anatomy folder, review raw MEG file) but i get the same error prompt every time.

I would appreciate your help,

Cheers,

Sean.

[Francois]

Hi Sean,

No I don’t know where this is coming from. In function bst_project_sources, it looks that the function tess_hemisplit is not returning the correct indices (you can explore this problem with the Matlab debugger if you are familiar with it).
Have you made sure that everything is imported properly in the subject anatomy?
For the file cortex_15000V, do you have an atlas “Structures” that contain two entries: “L Cortex” and “R Cortex”?

I can have a look at it if you send me the subject folder:

• remove all the unnecessary files, and keep only the average source file that you are trying to project
• right-click on the subject folder > File > Export subject
• upload the zip file somewhere (dropbox for instance) and send me the link in a separate email

Cheers,
Francois

[Kanad_Mandke]

Hi Francois,

I am getting a similar error message. In my case it is appearing for every subject.
Strange thing is that it worked when I projected the sources on MRI for the first instance then, closed the window and projected the sources on cortex and shifted back to MRI and started getting the error.

Just like Sean, I have computed :
Averaged trials
overlapping spheres
Noise covariance
Computed wMNE
Display on MRI

Error message:

---

** Error: Line 32: Index exceeds matrix dimensions.
**
** Call stack:
** >tess_interp_mri_data.m at 32
** >panel_surface.m>UpdateOverlayCube at 1815
** >panel_surface.m>UpdateSurfaceColormap at 1522
** >panel_surface.m>UpdateSurfaceData at 1435
** >bst_call.m at 28
** >macro_methodcall.m at 39
** >panel_surface.m at 38
** >bst_figures.m>FireCurrentTimeChanged at 813
** >bst_call.m at 28
** >macro_methodcall.m at 39
** >bst_figures.m at 59
** >panel_time.m>SetCurrentTime at 240
** >bst_call.m at 28
** >macro_methodcall.m at 39
** >panel_time.m at 30
** >figure_timeseries.m>FigureMouseUpCallback at 542
**

---

Secondly, (when it worked the first instance) even though the head model seems appropriate the activation is seen (concentrated) at the base of the brain when the experimental task is auditory oddball. With wMNE, dSPM & LCMV.
If this error is solved I might be able to post pictures so to give you a better idea.

Best,
Kanad

[Francois]

Hi Kanad,

This is not the same type of error as the one you are referring to.
In Sean’s case, it was due to the projection to the default anatomy (Colin27).
In your case it’s just the re-interpolation of the surface into the volume, it is probably a simpler problem.

The first thing you could try is to remove all the existing interpolations from the surface files.
In the anatomy view, right-click on the cortex file > Remove interpolations.
Let me know if you the error stays.
Have you tried just re-importing everything for this subject? Sometimes a manipulation error at some point can lead to strange errors.

Have you calculated the sources on the surface (like in the introduction tutorials) or in the volume (like in this tutorial: http://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource)?
If you are interested in unconstrained positions in the entire volume, you might be interested in the second option.
If you get errors or weird results, try first on a surface-based approach: because there are a lot more users for those methods, the code has been debugged a lot more over the years.

If you don’t manage to solve your problems, please post a few screen captures (showing the structure of your database, the MRI/sensor registration, the ERP…)
Alternatively, if you have subject that is not too big, you can send it to me: right-click on the subject > File > Export subject. Then upload the .zip file somewhere and send me the link by email (click on my username on this forum).

Cheers,
Francois

[Kanad_Mandke]

Hi Francois,

Thanks for clarifying.
I had already tried the remove interpolations options but the error was persistent. I was trying to avoid re-importing everything but I’ll just give that a go. Hope that sorts it out.

I am interested in the unconstrained positions based on the entire MR volume (second tutorial) but as you have suggested I’ll just try a surfaced based option, if that doesnt work i’ll send you an email.

Thanks again.
Kanad

[Francois]

Hi Kanad,

The MEG-MRI registration and the evoked responses look really good, you should be able to get correct source maps.

1. How do you use the .pos file? If it has the correct format (same as in the dataset of introduction tutorial), you just have to copy it inside the .ds folder and it should be used automatically. Don’t try to add it manually after linking the .ds folder to your database.
2. Can you post a screen capture that shows the head shape (green points) loaded from this .pos file
3. Where is this head surface coming from? The holes in it are probably preventing the automatic registration to work. Fix this before you try to re-load your data with the .pos file. Any particular reason for which you don’t use the head surface generated by Brainstorm?
4. Is your version of Brainstorm up-to-date (less than a month old)?
5. At the MNI, we don’t really use the normalized sLORETA solution. We prefer to use either Z-scored wMNE maps (or dSPM). We cannot provide much support regarding those results. Please post screen captures of your MNE and Z-scored MNE maps instead.
6. Are you sure your noise covariance matrix has been correctly estimated. A badly defined baseline / noise covariance is one common source of non-sense source maps. If the segments of recordings you used for estimating the noise covariance contain some of the brain activity of interest (in your case some auditory activity), the auditory cortex may tend to be excluded from your source reconstruction. This is why we always recommend to use a noise covariance calculated from empty room recordings, or resting state recordings.
7. I am currently working on an auditory tutorial, this may help you as well (the source part is not finished yet, but will be in the next few days):
   http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory

Cheers,
Francois

[Francois]

1. I initially had copied the .pos in the .ds folder before importing the data and got these results. After which I removed the file and integrated that through digitised head points --> add points (though I did notice, .pos is under EEG) which still gave the same results. For the previous post I completely removed the .pos file and computed the headmodels/mri alignment only based on fiducial, which still has given quite a good fit.

You can either leave the .pos file in the .ds folder (and say YES to the automatic registration), or just completely ignore it.
I would not add it after manually, as it doesn't do exactly the same thing.

2. Unfortunately, the stylus that we have is rather sluggish and hence it sometimes records unintended data points, 2 outliers. But Im sure those will be removed when refining the headshape. However, I have not used the digitised headshape (for the previous set of screenshots I did not use the .pos file). How do you suggest I check if the holes are really interfering? If then, how do I fix those?

This fitting process could be a bit biased by the outliers, you should remove them from the pos file manually.
They are easy to find, they are the two ones with the extreme values in X coordinates (press CTRL+A to see the axes)

3. We usually generate surfaces using some in house packages but on this occasion I have used BrainVisa (I dont have separated MR scans of the brain for all participants). I have imported those surfaces into BS and down sampled them before merging the surfaces (as mentioned in the tutorial).

I recommend you import the BrainVISA / FreeSurfer segmentation results with the menu "Import anatomy folder", as indicated in those tutorials:
http://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa
http://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer

5. Have you correctly removed the blinks from your recordings?

6. I was using the pre-stimulus interval to calculate the noise covariance. As per your recommendation, I have used an empty room recording to compute the covariance matrix and used that for further processing. This has improved the results slightly but the basal activity is still there. Although misplaced, the activation has now moved laterally.

Note that the noise recordings have to come from the same day.

7. I still think the problem is somewhere in the headshape/co-registeration.

The registration looks good, the helmet is correctly placed on the subject's head. If you have a registration problem here, it would not influence the results more than for a few millimeters in spatial accuracy.
I would tend to think it is more due to the modeling itself (noise covariance and/or inverse model).

[Francois]

Hi Kanad,

It is difficult to evaluate if the data was properly imported just by looking at your Brainstorm database.
Could you send me your original recordings as well?
(Empty room recordings + subject recordings + anatomy)

Thanks,
Francois

[Francois]

Hi Kanad,

1. I don’t have the segmentation of the MRI, so I just did the reconstruction on the Colin27 brain.
   Btw, I recommend you use FreeSurfer for the cortex segmentation, it generates more useful information than BrainVISA (atlases, subject co-registration, subcortical atlas):
   http://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer
   http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects

2. You didn’t include the .pos files in the datasets, so I wouldn’t have any accurate registration anyway (you should copy the .pos files in each and every .ds folder).
   You didn’t include the empty room recordings, so I calculated the noise covariance matrix with the pre-stim baseline.

3. I don’t recommend you use the averaged .ds folders, you should recalculate the averages in Brainstorm (but I think this is already what you’re doing, right?)

4. Are your EEG channels supposed to contain anything meaningful?

5. I would recommend using configuring your acquisition software to save continuous files, rather than epoched files. There is no way to apply correct frequency filters on epoched files (you have strong 50Hz and 150Hz noise), and it makes it also difficult to calculate SSP projectors. See the continuous tutorials on the website (introduction tutorials and auditory tutorial).

6. MLT23 is bad everywhere, make sure you didn’t include it in your source reconstruction.

7. Even with this very rough source reconstruction, I got really clean results for the N100 (see attached screen capture). The quality of your recordings is very good.
   The main problem you have is that you didn’t clean for blinks, saccades and heartbeats. And your subject seems to be moving his eyes a lot after the stim (didn’t you have a fixation cross?). Most of what is recorded after 300ms is eye movements, in both conditions. See the second screen capture. A lot of what you’re seeing at the poles of the frontal and temporal lobes is probably coming from eye movements. If you want clean results, you should clean your recordings. See what is done in our recent auditory tutorial:
   http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory

8. I would recommend you always add two bipolar electrodes in your acquisition to record the heart and the vertical EOG.
   Right now, we have no way of detecting and correcting heartbeats and blinks automatically.
   You can either go through all the trials and try to identify manually the blinks/saccades/heartbeats and then calculate SSP projectors. Or simply mark those trials as bad (but then you would remove 80% of them).
   Last option: apply a high-pass filter at 2Hz (or even higher), to get rid of the slow eye movements (but it will get rid of some of the P300 as well).

Cheers,
Francois

[Kanad_Mandke]

Hi Francois,

Thank you so much for your detailed reply.
This will definitely help me.

This specific recording is from a MEG naive subject and its one of the first measurements that I did. After I realised the shortcomings from this recording I have optimised the protocol even further. fixation cross, additional electrodes etc.,

3. Yes I am re-calculating all the averages in Brainstorm from the .ds (epoched) file.

4. The EEG channels in this case do not have anything. I’ll be adding Cz & Pz later.

5. should I use *.ds, convert it to continuous in Brainstorm and then import it like in the tutorial or use _AUX.ds instead?

6. yes, MLT23 has been marked out.

7. I had removed some eye blinks but maybe not all. I’ll try again with a stricter criterion.

8. Yes, bipolar electrodes will be added in the future recordings. Thanks for recommending that.
   Just to clarify what I understand, so once I link the raw file, i’ll go through the trials and mark the eye blinks and group them together. From there on will i be able to link the custom group in the SSP pipeline without the EOG channel? or should I identify the blinks on one particular MEG channel and use that in the SSP pipeline?
   Beyond this point, if needed I’ll add a high-pass filter.

Sorry for bothering you again, Im quite new to this area and still exploring everything.

Thanks,
Kanad

[Francois]

Hello

5. should I use *.ds, convert it to continuous in Brainstorm and then import it like in the tutorial or use _AUX.ds instead?

We use preferentially the AUX files, but if you set correctly the acquisition to have a continuous file in the regular .ds, it doesn't matter.
For example, the auditory tutorial uses "epoched" datasets.

Just to clarify what I understand, so once I link the raw file, i'll go through the trials and mark the eye blinks and group them together. From there on will i be able to link the custom group in the SSP pipeline without the EOG channel? or should I identify the blinks on one particular MEG channel and use that in the SSP pipeline?

You could do both: mark the events manually, or try to detect them on one frontal MEG channel where the blinks are very strong.
For the SSP calculation, all you need is a category of events that points at one precise artifact, it doesn't matter how this events have been marked or detected.

One the subject I looked at, given the amount of eye movements you have, you probably didn't have a fixation cross.
You can try with SSPs, but you may need a high-pass filter if it doesn't remove the artifacts correctly.

Cheers,
Francois

[Kanad_Mandke]

Hi Francois,

I have followed every step according to what you have suggested so far and what is mentioned in the tutorials but I am still getting predominant basal activation.

1. To start with, I linked the AUX file and did the spectral evaluation to remove 50Hz harmonics, mark some bad channels and segments.
   

   
   
   

2. Manually marked eye blinks, saccades and heart beats across all trials.
   

   
   
   
   Computed the SSPs according to the SSP tutorial. Cardiac first, blinks later and then a generic SSP for saccades.
   All the major components are 12%, 19% and 18% respectively. Specifically for saccades if I add a filter of 1Hz-2.5Hz the component weight increases upto 31% but that affects the p3 amplitude greatly. So I resorted to the 18% component. For blinks and saccades the sensor cap shows a strong dipolar pattern for frontal regions.

3. The averaged waveforms for deviant & standard
   

   
   
   

4. Source space (dSPM) averages for deviant and standard
   

   
   
   
   
   
   
   

5. MRI Co-reg for your reference
   

   
   
   

Since you got good localisation for N100, I am quite sure I have made a mistake somewhere but can't seem to isolate that.

Please let me know.

Best,
Kanad

[Francois]

1. The source maps you show at 240ms are due to the eye movements. I observe the exact same thing on my side. I don’t know how to process eye closed recordings.
2. Please post what you get at 100ms, so I can check if I get something similar
3. Please post the topographies of your all your selected SSP (in the Record tab, menu SSP > Select active projectors, then click on the button “Display topography”).

[Francois]

1. The SSP for the saccades is the same as the blink one. You should correct first for the blinks, then recalculate the SSP for the saccades with the option “Use existing SSP projectors”. It’s not going to be really single saccades as discussed in the tutorials, but very slow eye movements.
2. How come you identify “blinks” if this is an eye-closed experiment?
3. You should not process this dataset as continuous (I don’t know if you did). All the online tutorials are working with continuous files, which is not your case. You should not use the menu “convert to continuous files”. You have a file that is already epoched, you should process it as a list of epochs.
4. The PSD plot you posted looks really weird. To calculate the power spectrum from epochs: import all the epochs in the database, then select them all in Process1, run the process “FFT” with the option “Average output”
5. If you did something wrong, it is not in the source modeling: look how clean the evoked responses (sensor traces) I posted on August 12th are compared with the ones you just posted.
6. Make sure that when you imported your recordings, you corrected the DC offset based only on the baseline (-300ms to 0ms)
7. The power spectrum shows (attached here) that more sensors could be noisy: MLT13, MLF11, MZF01, MRF11, MLO31, MRO31
8. With 1.5s long epochs, you cannot run any decent high-pass filter that is lower than 2Hz
9. If this is a pilot, consider switching to an eyes-opened task with a fixation cross.

[Kanad_Mandke]

Hi Francois,

Thanks for your reply.

The SSP that I posted earlier, blinks & saccades though had same pattern had different component weights. I have always used ''use existing SSP projectors''
Here are the SSPs remarked:

Blinks 11%

Cardiac 9%

Saccadic 8%

2. Sorry if I didn't make it clear at the start, but it is an eye open experiment.
   Since it was the first run testing the entire setup, I didn't have a fixation cross. But yes, I have added that now with additional electrodes for future measurements.

3. I have processed the dataset in both continuous and epoched files.
   With _AUX.ds (previous screenshots) and *.ds today.

Here is what I have done so far:
Linked the epoched (*.ds) file, marked the events.
Computed the SSPs, blinks first, saccades later. Imported the recording as standard & deviant.
Computed FFT for both and marked the bad channels. Removed the power line contamination. Based on those, got the averages, which do look a lot cleaner.

FFT:

Averages: deviant & standard

Got the dSPM for both the conditions.
The localisation has slightly improved, in terms that it at least is now showing us activation in some what reasonable location. However, the eye related artefacts are still present. Interestingly, the activation seems to have 'lateralised' to the left side hemisphere.

Standard average

Deviant average

Lastly, the way I understand the procedure of generating dSPM is that we compute it for every trial and average it in the source space before displaying (induced responses?).
So is there a way to construct sources directly for the cleaner averaged waveform? This wont be as accurate as the method described in the tutorial but wont it get rid off the eye artefacts as those wont be time locked?

Thanks,
Kanad

[Francois]

Hi Kanad,

• Your averages look a lot cleaner. But all this mess at the end of the deviant average may indicate that you have a lot of eye movements left. Check your trials one by one, at this point you have no other option. The ocular artifacts (blinks or movements) are not time locked but they are huge, the amplitudes are so high that you need many hundreds of trials to have them disappear in the average.

• Your blink component looks ok, but I’m not really sure about the two others. The cardiac component may have some auditory or ocular activity in it. The saccade one contains some auditory activity. Try to refine your computation.

• After you calculate all your SSP projectors, review all the recordings manually again and mark as bad all the segments that still look noisy (select time segment and CTRL+B or right-click > Mark segment as bad). You still have some strong artifacts to remove.

• I see your averages are called “deviant | notch” and “average | notch”. This means that you applied a notch filter on the imported epochs. This is not a recommended operation. The edge effects of any frequency filter can be important, we only apply them on long continuous signals. If you have the AUX files, you should work only with them and do all the pre-processing and artifact cleaning on the entire sessions.

• Your cortex surface looks bad. What did you use to generate this? I would recommend you try with FreeSurfer or BrainSuite instead (check the tutorials online).

• About the averages: within one run (one channel file), you can compute a shared inversion kernel, calculate the average of the recordings per condition and use the source link of this averages. If the position of the head does not change: sources(average)=average(sources). Then if you want to average across runs or subjects, you need to average in source space for accurate results.

Good luck, you’re almost there =)
Francois

[Kanad_Mandke]

Hi Francois,

The SSPs and high pass filter worked like a charm. The filter has of course reduced the p3 response significantly but atleast Im getting fairly good localisation.
The last surface was generated using BrainVisa, even I noticed how bad it was, i'll switch to FreeSurfer. Until then, this is on Colin27.

Avg standard

Avg deviant

Thanks a lot for your quick replies. If you're ever in England, your drink is on me. =)

Cheers,
Kanad

[Francois]

Hi Kanad,
Glad we could help. You can also thank Beth Bock, the MEG engineer at McGill, she’s the local expert in artifact cleaning and she guided me for all those advices.
I take the drink offer seriously: we might be coming to the UK for a Brainstorm training some time next year =)
Francois

[Kanad_Mandke]

Brilliant. Looking forward to some Brainstorming in UK. =)
Thanks both of you! I’ll keep an eye for your updates.

Just a quick question, is there a way to convert the scout time series to a PSD plot?

Best,
Kanad

[Francois]

Do you mean: calculate the PSD for a signal you extract from a scout?
Yes, save the scout time series (process Extract > Scouts time series), then drag and drop the scout file to Process1 and run process Frequency > PSD.
To do it properly for one scout, you may want to calculate the PSD on all the source signals (set the scout function to ALL), then calculate the PSD, and finally average the power for each scout (process Average > Average rows).

Francois