fahrenfort / adam Goto Github PK

Hello,

Thank you for the toolbox !
I amy trying to run adam_detrend_and_epoch (Matlab R2018b, ADAM 1.13 and EEGLAB2021.0).

The function stops at this point:

When plotting temporal generalisation matrices, line 221 in adam_plot_MVPA seems to limit the number of plots to 12. This only happens when a plot order is specified, although when plotting temporal generalisation matrices, the line_colors argument does not seem relevant.

Hi Johannes, I ran my data with ADAM toolbox twice. First I had all subjects' filenames defined in the cfg.filenames, and second I defined only one subject. The results of the same subject turned out to be quite different. Why should this happen? Thanks.

Hello,

I am trying to run adam_detrend_and_epoch (Matlab R2018b, ADAM 1.13 and EEGLAB2021.0) on MEG data.

The function stops with this error:

[Undefined function or variable 'topcs'.

Error in nt_regw (line 78)
            if nargout>1; z(:,iChan)=x*(topcs*b(iChan,1:size(topcs,2))') + mn(:,iChan); end

Error in nt_detrend (line 87)
    [~,y]=nt_regw(x,r,w);

Error in detrend_and_epoch (line 236)
        [~, w2,~,regressline2] = nt_detrend(tmp,polynomial_order,w1); % then nth order with mask of previous
        step

Error in adam_detrend_and_epoch (line 148)
        detrend_and_epoch(datadir,filenames{cSubj},outputdir, start_epoch, end_epoch, polynomial_order,
        pad_length, start_mask, end_mask, mask_only_current, mask_bad_data, channelpool, remove_bad_chans,
        event_codes);

Error in script (line 23)
adam_detrend_and_epoch(cfg);](url)

Also, I have this warning several times before the function stops.

Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND =  1.030416e-07. 
> In nt_regw (line 76)
  In nt_detrend (line 87)
  In detrend_and_epoch (line 236)
  In adam_detrend_and_epoch (line 148)
  In script (line 23)

Do you have an idea of what is going wrong?

Thank you very much!

Greetings,

on http://www.fahrenfort.com/ADAM.htm one can download the toolbox after filling out a form. It says "Using the toolbox for medical purposes is prohibited."

I did not fill out the form, but found the toolbox here on GitHub (https://github.com/fahrenfort/ADAM/). The license distributed with the toolbox is GPLv3 (LICENSE.txt in the root directory), so I assume that is the applicable license.

The issue is that prohibiting medical use seems to be an additional term, which if I read the GPLv3 (see section 7 and 10) correctly, could be removed by recipients: "If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term"

That would make the prohibition rather pointless; I suggest you consider removing the prohibition altogether. If you are concerned about being sued, please note that the GPLv3 license already covers liability (section 16). If you are concerned about the software being used for medical purposes, please consider to include a notice such as done with AFNI (distributed under GPLv2+), see https://afni.nimh.nih.gov/pub/dist/src/README.copyright:

*** This software was designed to be used only for research purposes. ***
*** Clinical applications are not recommended, and this software has ***
*** NOT been evaluated by the United States FDA for any clinical use. ***

The crucial difference here is recommendation versus prohibition.

Thanks a ton for this awesome tool. The way my data was pre-processed, it only contains relevant epochs. However, possible event values vary across subjects. Is it currently possible to (i) either simply use all event values in a file or (ii) for the code to handle event values as possible but not necessary values? As I have not been able to identify, I would like to suggest this for an enhancement of the tool. Best, Christine

Hi,

I am doing some EEG processing and have found your tool to be very useful. There are however a few functionalities that can be useful but aren't implemented, I was wondering if there was a reasoning behind what you chose to include and exclude from your pipeline. Additionally, do you have any design recommendations/preferences if I was to implement these functionalities on my own and push a merge request?

1. Labs like Steven Luck's usually average multiple trials to increase signal-noise ratio, is there a way of doing this in ADAM? If not is there a theoretical reason?
2. Is there a way to average statistics of multiple classifiers? For instance, if one has 3 subjects and 4 orientations (60 deg, 120, 210, 330) but wants to decode only orientations that are 90 degrees apart (60 vs 330 and 120 vs 210) and do group level cluster-based permutation testing. Currently, we "double" the subjects and do a single classifier for 6 subjects, can the same result be achieved without this workaround?
3. Is there a way to load eeglab datasets directly in ADAM? currently, we convert these data to a MAT file, but I assume this functionality already exists and I just failed to figure it out.

Thank you very much!

I started testing your scripts on my data (.set already epoched, 2 classes). It keeps giving me the error: "Error using read_raw_data('The dimord field seems missing and/or dimensions in the dataset seem to be off. When you are using fieldtrip format, make sure the input files have dimord rpt_chan_time (trial x channel x time).')". I'm not using fieldtrip format. This occurs both using cfg.raw_or_tfr = 'tfr'; or 'raw'. So, I downloaded your data from https://osf.io/eh4u8 and tested on the script made available https://osf.io/chz37 and the very same error occurred. I'm currently using Matlab R2022b. What I'm missing?

Hi! Thanks for this wonderful toolbox. I have encountered an issue but I'm not sure whether it's an ADAM issue or a FieldTrip issue. In our lab, we use a 128-channel EEG system (Biosemi ActiveTwo) that has an ABC-radial layout (not the 10-20 layout!), and its channel labels are A1-A32, B1-B32, C1-C32, and D1-D32. Unfortunately, ADAM only recognises 8 of these channels (A1 A2 B1 B2 C1 C2 D1 D2). For this reason, I created a bundle in ADAM's select_channels script (I tried to attach the script here but GitHub doesn't let me). These are the relevant new lines:

bundlenames.BIOSEMI_128_ABC = {'A1' 'A2' 'A3' 'A4' 'A5' 'A6' 'A7' 'A8' 'A9' 'A10' 'A11' 'A12' 'A13' 'A14' 'A15' 'A16' 'A17' 'A18' 'A19' 'A20' 'A21' 'A22' 'A23' 'A24' 'A25' ... 'A26' 'A27' 'A28' 'A29' 'A30' 'A31' 'A32' 'B1' 'B2' 'B3' 'B4' 'B5' 'B6' 'B7' 'B8' 'B9' 'B10' 'B11' 'B12' 'B13' 'B14' 'B15' 'B16' 'B17' 'B18' 'B19' 'B20' 'B21' 'B22' 'B23' 'B24' 'B25' ... 'B26' 'B27' 'B28' 'B29' 'B30' 'B31' 'B32' 'C1' 'C2' 'C3' 'C4' 'C5' 'C6' 'C7' 'C8' 'C9' 'C10' 'C11' 'C12' 'C13' 'C14' 'C15' 'C16' 'C17' 'C18' 'C19' 'C20' 'C21' 'C22' 'C23' 'C24' 'C25' ... 'C26' 'C27' 'C28' 'C29' 'C30' 'C31' 'C32' 'D1' 'D2' 'D3' 'D4' 'D5' 'D6' 'D7' 'D8' 'D9' 'D10' 'D11' 'D12' 'D13' 'D14' 'D15' 'D16' 'D17' 'D18' 'D19' 'D20' 'D21' 'D22' 'D23' 'D24' 'D25' ... 'D26' 'D27' 'D28' 'D29' 'D30' 'D31' 'D32'}; % 128-channel Biosemi ABC system

I also created a channel location file - it's already contained in the EEG datasets, but I added it just in case (I also tried to attach this BESA file but GitHub doesn't let me):

% These are the EEG and EOG channels according to the radial ABC definition: if exist('biosemi_128_ABC_chanlocdata','file') load('biosemi_128_ABC_chanlocdata'); else chanlocdata = readlocs(trycapfile,'importmode','native'); % from ABC 128-electrode biosemi system end

Unfortunately, it didn't work. ADAM recognises that there are 128 channels, but it only selects those 8 channels I mentioned above (screenshot attached). Thanks so much for the help!

Renzo

One more suggestion for enhancement: it would be perfect if it was possible to limit the time window to be included in the first-level analyses. Often, epochs are longer than the time windows of interest.