[FieldTrip] fieldtrip atlas
RICHARDS, JOHN
RICHARDS at mailbox.sc.edu
Mon Mar 29 21:29:10 CEST 2021
I think the tutorial MRI might be an individual participant.
If you use the MNI head as your participant, there are about 30 stereotaxic atlases the fit the MNI head.
Its relatively easy to take a MRI volume stereotaxic atlas and transform it into fieldtrip type pos/inside files, where inside is the ROI number from the atlas
The pos in the atlas can be matched with the pos in the source volume with "ismember".
Once this match is made, you can read the atlas ROI for each voxel in the source volume directly from the "inside" values.
We have been using some matlab procs that we obtained from the fOLD NIRS program to do this.
e.g.
source.pos are the 3D locations (voxels) in a 1x1x1 source volume
atlas is a MRI volume read from an atlas.
ROI_atlas= fOLDMNICoordinates(atlas,atlas.ac*1000);
ROI_data=fOLDAddLandmark(source.pos,ROI_atlas,0);
ROI data will have each point on the atlas with the source.pos marked, and you can read the ROIs directly.
An alternative is to reverse the procedure, so that the ROI_data rows are each the source pos, and the final column will be the ROI number.
It takes a little programming to get this to work, but once done it generalizes to any stereotaxic atlas MRI volume (LPBA, Hammers, AAL, DTK, ....)
John
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John E. Richards
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Email: richards-john at sc.edu
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Today's Topics:
1. Re: Atlas compatible with the 15684 point sourcemodel mesh
(Schoffelen, J.M. (Jan Mathijs))
2. Re: baseline normalizing (mubeen afzal)
3. Re: baseline normalizing (Schoffelen, J.M. (Jan Mathijs))
4. Re: baseline normalizing (mubeen afzal)
5. Importing event files (mubeen afzal)
----------------------------------------------------------------------
Hi Fieldtrippers.
Is there a cortical atlas available to interpolate with the sourcemodel mesh described here?
https://protect2.fireeye.com/v1/url?k=1d8e2079-421518ad-1d8e6eb8-860a66ff9d26-0e432a46f37fc1f1&q=1&e=6f1b46a5-406b-4943-9409-43d04ab1350f&u=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F
I found the atlas_conte69_8196reg_LR_brodmann_subparc.mat atlas in the donders repository. Is this the most appropriate atlas to interpolate my sourcemesh with?
Best,
Paolo
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Paolo Belardinelli, PhD
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Message: 2
Date: Sun, 28 Mar 2021 13:52:12 +0000
From: mubeen afzal <mubafzal at hotmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] baseline normalizing
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Ahh perfect Tzvetan. Thanks alot for the quick reply. This function is good to transform the time series data.
Regards,
Mubeen
________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Tzvetan Popov <tzvetan.popov at uni-konstanz.de>
Sent: Sunday, March 28, 2021 10:48 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] baseline normalizing
Dear Mubeen,
The function you intend to use requires time dimension. What you provide is only power spectrum.
You could use https://protect2.fireeye.com/v1/url?k=232124d8-7cba1c0c-23216a19-860a66ff9d26-039ed9e601fb4800&q=1&e=6f1b46a5-406b-4943-9409-43d04ab1350f&u=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Freference%2Fft_preproc_standardize%2F prior to your freqanalysis if standardized z-scores is what you need.
Good luck,
Tzvetan
Am 3/28/21 um 07:16 schrieb mubeen afzal <mubafzal at hotmail.com>:
Hi all,
In brainstorm there is option of baseline normalizing (zscore or db or other methods) the timeseries epochs/trials of interest before frequency analysis allowing visual comparisons and further frequency analysis of the normalized epochs
The normalization function function [freq] = ft_freqbaseline(cfg, freq) doesnt allow normalizing a freq output dimord structure with chan_freq derived using 'mtmfft' method
I get this error message -
"the call to "ft_freqanalysis" took 1 seconds the input is freq data with 21 channels, 191 frequencybins and no timebins Error using ft_freqbaseline (line 146) unsupported data dimensions: chan_freq"
Is there a way around this?
Thanks all.
Mubeen
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Message: 3
Date: Sun, 28 Mar 2021 14:23:09 +0000
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] baseline normalizing
Message-ID: <E966E48E-E276-48D7-A04A-E5F4E2131A09 at donders.ru.nl>
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Just one addition to Tzvetan’s reply, just for future reference:
ft_preproc_standardize is a rather ‘low-level’ function, and not recommended unless you know what you’re doing.
For your purpose you probably want to use ft_channelnormalise or ft_denoise_prewhiten. Which of the two depends on what you think is happening in Brainstorm. Note that the former (i.e. ft_channelnormalise) only scales the data (and the resulting power spectra if you proceed with spectral analysis), so it is not really clear what you intend to achieve.
Best wishes,
Jan-Mathijs
On 28 Mar 2021, at 15:52, mubeen afzal <mubafzal at hotmail.com<mailto:mubafzal at hotmail.com>> wrote:
Ahh perfect Tzvetan. Thanks alot for the quick reply. This function is good to transform the time series data.
Regards,
Mubeen
________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Tzvetan Popov <tzvetan.popov at uni-konstanz.de<mailto:tzvetan.popov at uni-konstanz.de>>
Sent: Sunday, March 28, 2021 10:48 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] baseline normalizing
Dear Mubeen,
The function you intend to use requires time dimension. What you provide is only power spectrum.
You could use https://protect2.fireeye.com/v1/url?k=732ccd5b-2cb7f58f-732c839a-860a66ff9d26-d976de38571f8062&q=1&e=6f1b46a5-406b-4943-9409-43d04ab1350f&u=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Freference%2Fft_preproc_standardize%2F prior to your freqanalysis if standardized z-scores is what you need.
Good luck,
Tzvetan
Am 3/28/21 um 07:16 schrieb mubeen afzal <mubafzal at hotmail.com<mailto:mubafzal at hotmail.com>>:
Hi all,
In brainstorm there is option of baseline normalizing (zscore or db or other methods) the timeseries epochs/trials of interest before frequency analysis allowing visual comparisons and further frequency analysis of the normalized epochs
The normalization function function [freq] = ft_freqbaseline(cfg, freq) doesnt allow normalizing a freq output dimord structure with chan_freq derived using 'mtmfft' method
I get this error message -
"the call to "ft_freqanalysis" took 1 seconds the input is freq data with 21 channels, 191 frequencybins and no timebins Error using ft_freqbaseline (line 146) unsupported data dimensions: chan_freq"
Is there a way around this?
Thanks all.
Mubeen
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https://doi.org/10.1371/journal.pcbi.1002202
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Message: 4
Date: Sun, 28 Mar 2021 15:37:45 +0000
From: mubeen afzal <mubafzal at hotmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] baseline normalizing
Message-ID:
<DB7PR06MB4952D15E71B15D9664E64473C57F9 at DB7PR06MB4952.eurprd06.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
Hi Jan,
Thanks for this added info. This (ft_channelnormalise) appears like a good function for my power analysis because it provides the perchannel vs across channel added option. I have not been sure in brainstorm whether the baseline values being used as input to z-transform was derived from all channels or per respective channel. I think 'all channels' will be more appropriate as I am looking at abrupt discharges which dont necessarily channel by channel follow the resting state baseline rhythm variation. For example frontal regions have more faster lower amplitude but the discharges of my interest have higher amplitude frontally. Makes it tricky.
I see however there is no segment definition input in this function for baseline selection which makes preproc_standardize good. My understanding was that baseline for transforming is always better selected 'out of' the segment to be analysed. I will test and try and see both functions.
Regards,
Mubeen
________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl>
Sent: Sunday, March 28, 2021 5:23 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] baseline normalizing
Just one addition to Tzvetan’s reply, just for future reference:
ft_preproc_standardize is a rather ‘low-level’ function, and not recommended unless you know what you’re doing.
For your purpose you probably want to use ft_channelnormalise or ft_denoise_prewhiten. Which of the two depends on what you think is happening in Brainstorm. Note that the former (i.e. ft_channelnormalise) only scales the data (and the resulting power spectra if you proceed with spectral analysis), so it is not really clear what you intend to achieve.
Best wishes,
Jan-Mathijs
On 28 Mar 2021, at 15:52, mubeen afzal <mubafzal at hotmail.com<mailto:mubafzal at hotmail.com>> wrote:
Ahh perfect Tzvetan. Thanks alot for the quick reply. This function is good to transform the time series data.
Regards,
Mubeen
________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Tzvetan Popov <tzvetan.popov at uni-konstanz.de<mailto:tzvetan.popov at uni-konstanz.de>>
Sent: Sunday, March 28, 2021 10:48 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] baseline normalizing
Dear Mubeen,
The function you intend to use requires time dimension. What you provide is only power spectrum.
You could use https://protect2.fireeye.com/v1/url?k=56799887-09e2a053-5679d646-860a66ff9d26-6f60023ab075e528&q=1&e=6f1b46a5-406b-4943-9409-43d04ab1350f&u=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Freference%2Fft_preproc_standardize%2F<https://protect2.fireeye.com/v1/url?k=fa28ce07-a5b3f6d3-fa2880c6-860a66ff9d26-88d48c5e93284f0e&q=1&e=6f1b46a5-406b-4943-9409-43d04ab1350f&u=https%3A%2F%2Femea01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fwww.fieldtriptoolbox.org%252Freference%252Fft_preproc_standardize%252F%26data%3D04%257C01%257C%257C50500c0f02d049d45c2308d8f1f84540%257C84df9e7fe9f640afb435aaaaaaaaaaaa%257C1%257C0%257C637525396099670134%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Dts%252Fb%252BIy0goudTeiglpck7bhc0c7HaKmwMmAVUlsqR34%253D%26reserved%3D0> prior to your freqanalysis if standardized z-scores is what you need.
Good luck,
Tzvetan
Am 3/28/21 um 07:16 schrieb mubeen afzal <mubafzal at hotmail.com<mailto:mubafzal at hotmail.com>>:
Hi all,
In brainstorm there is option of baseline normalizing (zscore or db or other methods) the timeseries epochs/trials of interest before frequency analysis allowing visual comparisons and further frequency analysis of the normalized epochs
The normalization function function [freq] = ft_freqbaseline(cfg, freq) doesnt allow normalizing a freq output dimord structure with chan_freq derived using 'mtmfft' method
I get this error message -
"the call to "ft_freqanalysis" took 1 seconds the input is freq data with 21 channels, 191 frequencybins and no timebins Error using ft_freqbaseline (line 146) unsupported data dimensions: chan_freq"
Is there a way around this?
Thanks all.
Mubeen
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Message: 5
Date: Sun, 28 Mar 2021 23:59:10 +0000
From: mubeen afzal <mubafzal at hotmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: [FieldTrip] Importing event files
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Hi to all fieldtrip experts,
My question today is there a way to import events from a simple .csv or .txt file done externally (brainstorm or edfbrowser) into the cfg, data event structure of fieldtrip and getting rid of previous annotations. Is all the event related information after preprocessing only in cfg.event and data.cfg.event structures or are there are other event related info in the fieldtrip configurations which I need to adjust as well? I have attached the brainstorm event export template.
Asking mainly because exporting events/annotations files from an external software is much faster then exporting/importing edf files.
Thanks to all for help on all my questions. Much appreciated.
Regards,
Mubeen
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