[FieldTrip] Replacing artifacts part by nan value

[Schoffelen, J.M. (Jan Mathijs)]

At the risk of asking the obvious: have you 'selected and marked as artifact segments of data’ while interacting with the figure that pops up when you call ft_databrowser?

Best wishes,
Jan-Mathijs

On 5 May 2024, at 20:33, Erfan Vi via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hi Jan Mathijs,

Hello, I apologize for the late reply
I corrected the spelling mistake but it didn't make any difference

Best wishes,
Erfan

On Tue, Aug 8, 2023 at 12:51 PM Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
Hi Erfan,

Could it be that there is a typo here?

cfg.artifactdef = cfg_artfctdef -> cfg.artfctdef = cfg_artfctdef;

Best wishes,
Jan-Mathijs

On 24 Jul 2023, at 08:43, Erfan Vi via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear FieldTrip users,
I use the  ArtifactMEG.zip<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdownload.fieldtriptoolbox.org%2Ftutorial%2FArtifactMEG.zip__%3B!!HJOPV4FYYWzcc1jazlU!4vKXD91CTmKqghFOD3Hgu_P6uxQdXXMKO4yQwwLLlgsOkdwBZ385rFZK23er0FM8P4cEUSNk0NW_7HzsUvmxaFOIew%24&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C6d475665c2cc4e85d8d808dc73db1fe4%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638512632212798218%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=X2gppSIoFzaiOksQ4gjuIvAzEwfv1R5i%2FW%2F7OCOzhso%3D&reserved=0> example MEG dataset and code in the link https://www.fieldtriptoolbox.org/tutorial/ica_artifact_cleaning/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fica_artifact_cleaning%2F__%3B!!HJOPV4FYYWzcc1jazlU!4vKXD91CTmKqghFOD3Hgu_P6uxQdXXMKO4yQwwLLlgsOkdwBZ385rFZK23er0FM8P4cEUSNk0NW_7HzsUvmxQBI3Lw%24&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C6d475665c2cc4e85d8d808dc73db1fe4%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638512632212798218%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=lnVQ3q4OfzFjZW2ZTtqjNaQJiMl2qf%2BI%2FxT46kx0FIU%3D&reserved=0> to remove the artifact as follows:
cfg = [];
cfg.continuous = 'yes';
cfg.blocksize = 60;
cfg.plotevents = 'no';
cfg.preproc.demean  = 'yes';
cfg.layout = 'CTF151.lay';
cfg = ft_databrowser(cfg, data);
cfg_artfctdef = cfg.artfctdef;

cfg = [];
cfg.artifactdef = cfg_artfctdef;
cfg.artfctdef.reject = 'nan';
data_clean = ft_rejectartifact(cfg, data);

For two reasons, the specified regions of the artifact are not replaced by the null value:
1) The output printed in the command window is:
rejected   0 trials completely
rejected   0 trials partially
filled parts of   0 trials with NaNs
filled parts of   0 trials with the specified value
resulting   1 trials
the call to "ft_rejectartifact" took 1 seconds
2) When I use the ft_databrowser function again for data_clean, basically the areas replaced with the null value should be invisible, which is not the case.
Can anyone explain to me what's the problem?
Thank you,
Erfan Vajdi
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https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!5Elnov9n-jvdLZPJJ37SCY8838Vwb8g8vIJRVIkVY7LptSOmvV34t0KzX4srA9AfkpIhoWGHJfaHl0EV3aOz5ftlbI0xDb1XBiTiPA$<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202__%3B!!HJOPV4FYYWzcc1jazlU!5Elnov9n-jvdLZPJJ37SCY8838Vwb8g8vIJRVIkVY7LptSOmvV34t0KzX4srA9AfkpIhoWGHJfaHl0EV3aOz5ftlbI0xDb1XBiTiPA%24&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C6d475665c2cc4e85d8d808dc73db1fe4%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638512632212798218%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=CLdGa6gFZeFnX3t3ZCqDUV0roLqlDmbxGXFZ8d8OIn8%3D&reserved=0>

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https://doi.org/10.1371/journal.pcbi.1002202<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C6d475665c2cc4e85d8d808dc73db1fe4%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638512632212798218%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=qTMYhvgp9aE2cU7uterUIyG%2BBr5v2bmT6BsdVcCWTOQ%3D&reserved=0>
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https://doi.org/10.1371/journal.pcbi.1002202

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