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Chat for Live Brainstorm workshop and Q&A: May 27, 2021
09:58:35 From Sylvain Baillet To Everyone:
Hi everyone and welcome! We’ll be starting shortly.
10:30:13 From Shresth Prasad To Everyone:
Can I assume that mne python is a subset of Brainstrom ?
10:30:56 From Sezen Asan To Everyone:
Will we have access to the powerpoint after the presentation? I am slow to take notes...
10:32:03 From Gabriela Cintra Januário To Everyone:
Good morning! Are you going to talk also about NIRSTORM?
10:32:49 From Kirandeep Kaur To Everyone:
I have been using brainstorm to compute functional connectivity in epilepsy subjects. I would like to understand what the threshold values indicate in the connectivity plots, how do we interpret them. Thanks!
10:33:20 From Gabriela Cintra Januário To Everyone:
Thank you!
10:34:30 From Sylvain Baillet To Everyone:
Brainstorm’s Youtube channel: https://www.youtube.com/channel/UCPXmMBgSZCRgfKBDtHKb77Q
10:35:01 From Sylvain Baillet To Everyone:
@Kirandeep: we have a new tutorial coming up for connectivity, including updated visualization tools:
10:35:22 From Sylvain Baillet To Everyone:
https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity2
10:36:06 From Sylvain Baillet To Everyone:
And about the connectivity graphs: https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph
10:36:21 From Sylvain Baillet To Everyone:
[ will be released over next few days ]
10:36:23 From Laura Globig To Everyone:
Thank you for the excellent documentation. Maybe a bit of a specific question too - but I have preprocessed my data in Brainstorm and now want to compute GLMs in SPM. To do that I need to export the time-frequency data into an SPM compatible format. From what I understand Brainstorm only permits export to SPM as volume source maps or surfaces. The alternative I found was exporting to field trip and then using spm_eeg_ft2spm (data, fname). But by exporting from Brainstorm I am losing quite a bit of relevant information e.g.,sensor positions and triggers. Is there a better way to export the data to SPM to make it suitable for further analysis? I
10:39:20 From Sylvain Baillet To Everyone:
@Laura: it should be possible directly from Brainsto=rm. Please see the following forum post: https://neuroimage.usc.edu/forums/t/export-source-space-time-frequency-maps-obtained-in-brainstorm-to-spm8-12/1697
10:40:36 From Sylvain Baillet To Everyone:
To everyone interested, there’s a specific doc on exporting to SPM: https://neuroimage.usc.edu/brainstorm/ExportSpm8
10:40:50 From Mohamed Ouardouz To Everyone:
Hello, I have tried brainstorm to analyse electrophysiological data from animals LFP. I know that Neuralynx file can be loaded into brainstorm but is there a way that I can take advantage of all the analysis tools brainstorm offer (like combining single unit with behavioral data to do some place cell analysis).
10:41:50 From Sylvain Baillet To Everyone:
@Shresth: not at all ;) It’s just that we design Brainstorm as a hub connected to many toolkits in the field.
10:43:05 From Kirandeep Kaur To Everyone:
@Sylvain Thanks ! :)
10:43:17 From Sylvain Baillet To Everyone:
@Mohamed: yes. please consult the specialized tutorial section: https://neuroimage.usc.edu/brainstorm/e-phys/Introduction
10:43:38 From Laura Globig To Everyone:
@Sylvain: Thank you! I will try this
10:43:48 From Sylvain Baillet To Everyone:
and the following paper: https://www.nature.com/articles/s41597-019-0242-z
10:44:47 From Takfarinas Medani To Everyone:
@Shresth, the MNE python is not a subset of Brainstorm, you can check this discussion about Brainstorm-MNE : https://neuroimage.usc.edu/forums/t/best-way-to-export-to-mne-python/12704
10:45:45 From Mohamed Ouardouz To Everyone:
Thanks I will. When it good we want more.
10:47:59 From Shresth Prasad To Everyone:
Can I work with Brainstrom without any prior knowledge about computer language or I should learn any language ?
10:48:38 From Sylvain Baillet To Everyone:
As you can see from the demo, you can access all functionalities via graphical user interactions.
10:49:07 From Sylvain Baillet To Everyone:
For those familiar with Matlab, they can also call brainstorm functions from scripts.
10:49:22 From Aaron Mohammed To Everyone:
Hello, are there any Brainstorm functions or MEX functions included with Brainstorm that can read raw cnt files and extract information like subject ID or date of creation?
10:50:39 From Sylvain Baillet To Everyone:
Yes, Brainstorm can read Neuroscan (.cnt, .eeg, .avg, .dat). For the specific function call, please post your request on the user forum - thanks!
10:51:43 From Aaron Mohammed To Everyone:
Okay thank you!
10:51:51 From Laura Globig To Everyone:
Related to data cleaning: How would you weigh off the benefit of manual artifact detection/data cleaning vs achieving easily reproducible results through using an automatic process?
10:52:21 From Laura Globig To Everyone:
(Especially if there are no separate blink channels in the MEG dataset)
10:53:39 From Sylvain Baillet To Everyone:
@Laura: we encourage the automatic detection and removal of artifacts, but quality of the outcome needs to be ascertained manually (at least in part).
10:54:05 From Sylvain Baillet To Everyone:
@Laura: if you do not have access to EOG channels, usually frontal sensors can work as surrogates.
10:54:32 From Graciela Catalina Alatorre Cruz To Everyone:
Brainstorm can separate or identify those events with correct and incorrect answers of participants?
10:54:54 From Laura Globig To Everyone:
Thank you! That is what have done thus far.
10:55:38 From Sylvain Baillet To Everyone:
@Graciela: if correct/incorrect is encoded with distinct events from the acquisition system, yes.
10:55:59 From Chaitanya Ganne To Everyone:
How do we baseline normalize data in Brainstorm? (I have seizure data, i.e., 10min before seizure and 10min after seizure... and I want to use the 10min before seizure as the baseline window.
10:57:43 From Sylvain Baillet To Everyone:
@Chaitanya: it depends on the measures you want to extract. Raymundo will show some of the possible strategies. For instance, you can specify baselines for centering, z-scoring, spectral normalization etc. from data segments in the same or different files.
10:58:25 From Chaitanya Ganne To Everyone:
Thank you. Exactly what I am looking for.. that would be very helpful..
11:01:09 From Chaitanya Ganne To Everyone:
Another question: Is ePrime event format supported in Brainstorm.
11:02:14 From sanaz khosravani To Everyone:
Would you please cover source localization as well?
11:02:47 From Sylvain Baillet To Everyone:
@chaitanya: it depends on which EEG/MEG acquisition system you are using, as eprime event codes will be stored in that file. Brainstorm supports a very diversified range of formats.
11:02:58 From Sylvain Baillet To Everyone:
@sanaz: yes, coming up!
11:03:04 From sanaz khosravani To Everyone:
Thank you!
11:03:42 From Chaitanya Ganne To Everyone:
Behavioral data is stored in EPrime software output format.
11:05:01 From Chaitanya Ganne To Everyone:
SEEG is saved in Nihon Kohden... but I convert them to EDFs for analysis. I was more interested in being able to use the EPrime behavioural data.
11:06:18 From Sylvain Baillet To Everyone:
You need to make sure the eprime behavior is captured with the identical time stamps as your SEEG. Hence they are typically recorded along the SEEG data, channeled into the NK acquisition system. Not an option for you?
11:11:08 From Chaitanya Ganne To Everyone:
Yes
11:11:10 From Chaitanya Ganne To Everyone:
It was me
11:11:57 From Chaitanya Ganne To Everyone:
yes
11:14:04 From Oscar Angulo To Everyone:
Would you change anything about the normalization protocol if you were looking at data from subjects across different days/sessions? Say the baseline activity is very different between sessions
11:14:28 From Chaitanya Ganne To Everyone:
Thank you experts. This was what I was looking for.
11:14:38 From Chaitanya Ganne To Everyone:
I will try this on my data and update you.
11:15:41 From Sylvain Baillet To Everyone:
@oscar: we need to bear in mind that the choice of a baseline is a significant decision, which needs to be motivated by a specific neuroscience question behind the study. Hence there is no generic answer;)
11:16:31 From Sylvain Baillet To Everyone:
In your case, maybe you want to use the first visit data as baseline to track changes across sessions, if you’re doing at a learning study.
11:17:40 From Sylvain Baillet To Everyone:
Follow us on Twitter ;) https://twitter.com/brainstorm2day
11:18:43 From Sylvain Baillet To Everyone:
Thanks Elena ;)
11:19:03 From Oscar Angulo To Everyone:
Thank you, Sylvain. Yes, it is to track changes to event-related activity with months of time in between sessions.
11:20:13 From Sylvain Baillet To Everyone:
@Oscar: if this is an ERP study, then prestim baseline could be one approach. Then you can separately assess changes in the very baseline across sessions, via a spectral analysis for instance, as Raymundo is showing now.
11:21:56 From Oscar Angulo To Everyone:
Thank you!!
11:26:01 From Chaitanya Ganne To Everyone:
It would be amazing if this video can be posted on youtube. You are giving some suggestions, seem simple but they are valuable practical tips.
11:27:39 From Aaron Mohammed To Everyone:
Will it still be possible to save figures in headless mode?
11:27:43 From Sylvain Baillet To Everyone:
Thanks! We already have an equivalent video already there from last year.
11:27:45 From Qianru Xu To Everyone:
Thanks for the detailed introduction and this handy tools! Have you mentioned before that you have some ready-made pipelines on your website? May I know where could I find them?
11:27:58 From Sylvain Baillet To Everyone:
@Aaron: yes.
11:28:37 From Sylvain Baillet To Everyone:
@Qianru: thanks! and yes, the data and pipelines are available from Brainstorm’s download page
11:28:47 From Conor Thornberry To Everyone:
Hi guys, would the initial process be the same with EEG data - particularly artefact removal and applying filters i.e. should you use ICA rather than the automatic SSP function or is it fine to use either?
11:28:57 From Aaron Mohammed To Everyone:
Okay thank you
11:29:23 From Sylvain Baillet To Everyone:
@Conor: yes, all tools apply to EEG, MEG and other forms of e-phys data.
11:29:45 From Qianru Xu To Everyone:
Thanks a lot!
11:29:57 From Takfarinas Medani To Everyone:
@Qianru, there is also more documentation on scripting here : https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting?highlight=%28script%29
11:30:03 From Conor Thornberry To Everyone:
Brill Sylvain, thanks!
11:30:20 From Sylvain Baillet To Everyone:
EEG users are indeed more familiar with ICA, and Brainstorm call EEGLab’s ICA functions and others.
11:34:45 From Qianru Xu To Everyone:
@Takfarinas Thank you so much!
11:37:09 From Mohamed Ouardouz To Everyone:
Hello, I uploaded continuous neuralunx electrophy data to brainstorm. I tried to generate an LFP data but it says Data type mismatch. any way to make it work.from raw
11:37:11 From Edouard Delaire To Everyone:
Is it possible to clean/analyze EEG data acquired during EEG-fMRI ?
11:38:00 From Sylvain Baillet To Everyone:
@mohamed: should work. please post your question to the forum and try to have a portion of your data accessible from somewhere for us to look into, e.g. dropbox etc.
11:38:37 From Mohamed Ouardouz To Everyone:
I will. Thanks
11:38:41 From Isil Bilgin To Everyone:
it is not a question but I wanted to acknowledge that, I have been using a lot of tools over the time being for all sort of neuroimaging analysis but how Brainstorm considers regarding all these inclusivity and reproducibility aspects of data analysis are really fascinating. I salute all the effort and thoughts goes behind it as a member coming from a community which tries to advocates such practices across the worldwide research groups for such a long time (a.k.a Brainhack Global)!
11:38:57 From Sylvain Baillet To Everyone:
@Edouard: in principle yes, but we do not feature a specific cleaning toolbox to that end. if you know of one that you’d like to see plugged in Brainstorm, please let us know (forum)
11:39:47 From Sylvain Baillet To Everyone:
@Isil: THANK YOU!!!!!
11:40:25 From Isil Bilgin To Everyone:
Thank you all \o/
11:42:21 From Payal Gupta To Everyone:
Hello,
11:43:20 From Payal Gupta To Everyone:
what is shows these correlation values ?
11:44:07 From Kirandeep Kaur To Everyone:
Thank you! that was great. I did not know the thresholds vary only between 0 and 1, makes sense now. Would really look forward to a connectivity workshop!
11:44:32 From Edouard Delaire To Everyone:
ok; Thanks you Sylvain. I am curently learning how to use EEGlab. I’ll try to look if it might be easy to integrate with brainstorm and if it is the case; will post in brainstorm forum
11:46:21 From A Ankeeta To Everyone:
hi everyone I am very new to MATLAB and I want to learn to write scripts how can I learn it as some of the things I was not able to understand
11:46:26 From Payal Gupta To Everyone:
Okay.. Thank you
11:47:27 From Sylvain Baillet To Everyone:
@Ankeeta: there is lot of online documentation around Matlab, including coding tutorials etc.
11:50:29 From Raymundo Cassani To Everyone:
https://github.com/brainstorm-tools/brainstorm3
11:50:56 From Raymundo Cassani To Everyone:
https://neuroimage.usc.edu/forums/
11:51:04 From LUCAS TRAMBAIOLLI To Everyone:
This toolbox is amazing, and Raymundo's tutorial made me much more confident to use it! Thank you very much!!
11:54:58 From Raymundo Cassani To Everyone:
Brainstorm workshop in Spanish: https://neuroimage.usc.edu/brainstorm/WorkshopZoom2021spa
11:54:59 From Chaitanya Ganne To Everyone:
Thank you so much for the great teaching session and for answering our questions.
11:55:57 From Qianru Xu To Everyone:
Thank you so much for all these considerations! That's so nice!
11:56:47 From Tracy Wu To Everyone:
Thank you Raymundo!
11:57:07 From Payal Gupta To Everyone:
great demonstration!
11:57:10 From Andre Pereira To Everyone:
Thank you so much!!
11:57:11 From Oscar Angulo To Everyone:
Gracias Raymundo!
11:57:15 From Conor Thornberry To Everyone:
Big thanks Raymundo and Sylvain, very clear and really informative!
11:57:19 From Marie McCusker To Everyone:
Thank you both!
11:57:22 From Laurence Chouinard To Everyone:
Thank you very much for this so interesting and useful session !
11:57:23 From Andre Pereira To Everyone:
Im also a Portuguese speaker
11:57:23 From Graciela Catalina Alatorre Cruz To Everyone:
Gracias Raymundo :)
11:57:50 From Isil Bilgin To Everyone:
Thank you all and the team! Hope to see more of these trainings in the future!
11:58:00 From A Ankeeta To Everyone:
This demo is really good and very useful.Thank you
11:58:19 From Gabriela Cintra Januário To Everyone:
Im also a Portuguese speaker (Brasil)
11:58:40 From Gabriela Cintra Januário To Everyone:
Obrigada Raymundo!
11:59:07 From Raymundo Cassani To Everyone:
Thanks everyone for attending the workshop/demo :)
11:59:08 From Mohamed Ouardouz To Everyone:
thanks both.
11:59:17 From Chaitanya Ganne To Everyone:
Thanks. Bye
11:59:18 From Fernando Lopez To Everyone:
Thank you!
11:59:52 From Andre Pereira To Everyone:
Thank you looking forward to put in practice
11:59:53 From Sylvain Baillet To Everyone:
@Isil: would be great - feel free to contact me as well.
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