[FieldTrip] using T1 and T2 for head model
RICHARDS, JOHN
RICHARDS at mailbox.sc.edu
Mon May 27 12:58:42 CEST 2019
Paolo.
There is nothing in the FT pipeline methods that uses T1 and T2 directly for the head model. I use a method that
1--Uses manual code and FSL to extract the brain (skull stripping)
2--Uses T1 and T2 with FSL's bet (bet2, betsurf) and the extracted brain to get skull and scalp segments
3--Uses the T2 for an estimate of CSF
4--Uses the T2 for the eye locations
5--Uses FSL fast on the brain for GM/WM
With this I construct a segmented MRI volume that consists of skin, skull, GM, WM, T2W-derived CSF, eyes, and other materials inside the head. This MRI volume can be read into FT for the head model for a full FEM model with the "fem-simbio" method.. It also provides the materials to identify the parts of a BEM compartment model (e.g., skin, skull, CSF, brain) that may be used with FT "bem-dipoli" method. These methods are unique in that they allow us to do full segmenting and head models on "developmental populations" (e.g., infants, children) that require special processing or "age-appropriate average templates" to use the tools designed for adult participants. We have outlined these steps in supplemental information accompanying several publications. We have recently figured out how to add "anisotropic WM conductivity" to the head models and are testing the influence of that on our results.
John
Richards, J.E., Gao, C., Contes, S., Guy, M., and Xie, W. (2018). Supplemental information for the neural sources of N170: Understanding timing of activation in face-selective areas. Unpublished paper available at ResearchGate (https://www.researchgate.net/). DOI: https://doi.org/10.13140/RG.2.2.15716.01924; Table 7 in https://jerlab.sc.edu/wp-content/uploads/2018/10/Experiment99-fMRI-and-ERP-Sources-Supplemental-Information.pdf.
Buzzell, G. A., Richards, J. E., White, L. K., Barker, T. V., Pine, D. S., & Fox, N. A. (2017). Supplemental Information for Development of the error-monitoring system from ages 9–35: unique insight provided by MRI-constrained source localization of EEG. Neuroimage. doi:https://doi.org/10.1016/j.neuroimage.2017.05.045 https://jerlab.sc.edu/wp-content/uploads/2018/12/Experiment-96-Supplemental-Information.pdf
Guy, M. W., Zieber, N. and Richards, J. E. (2016; Supplemental Information), The Cortical Development of Specialized Face Processing in Infancy. Child Development. Doi: 10.1111/cdev.12543 https://jerlab.sc.edu/wp-content/uploads/2018/12/Experiment-78-Cortical-development-of-face-processing-Supplemental-Information.pdf
Richards, J.E. (2013). Cortical sources of ERP in the prosaccade and antisaccade eye movements using realistic source models (Supplemental Information). Frontiers in Systems Neuroscience, 7:27. doi: 10.3389/fnsys.2013.00027 https://jerlab.sc.edu/wp-content/uploads/2018/07/expt50-73Supplemental.pdf
***********************************************
John E. Richards
Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC 29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu
https://jerlab.sc.edu
*************************************************
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Today's Topics:
1. Processing T1 and T2 weighted MR images with Fieldtrip
(Paolo Belardinelli)
2. Re: Processing T1 and T2 weighted MR images with Fieldtrip
(Schoffelen, J.M. (Jan Mathijs))
3. Re: Processing T1 and T2 weighted MR images with Fieldtrip
(Paolo Belardinelli)
4. Re: Processing T1 and T2 weighted MR images with Fieldtrip
(Schoffelen, J.M. (Jan Mathijs))
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Message: 1
Date: Sun, 26 May 2019 15:46:11 +0200
From: Paolo Belardinelli <paolo.belardinelli at gmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: [FieldTrip] Processing T1 and T2 weighted MR images with
Fieldtrip
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<CAMa54+PwxMz8xoDEGOwhHQ5GknVnrSt+_rbOLD8e2aBVxdc+ew at mail.gmail.com>
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Dear FieldTrippers,
is there a way to process simultaneously T1w and T2w MR images in Fieldtrip (in line with the mri2mesh function of SimNibs)? To my understanding this is currently not possible with ft_read_mri. Am I wrong?
Best,
Paolo Belardinelli
--
--
Paolo Belardinelli, PhD
Neurology Department
University Hospital Tuebingen
Eberhard Karls University Tuebingen
Hoppe-Seyler Str. 3
D-72076 Tuebingen
Tel: +49 7071 / 29 80478
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Message: 2
Date: Sun, 26 May 2019 15:04:22 +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] Processing T1 and T2 weighted MR images with
Fieldtrip
Message-ID: <AE5DEFFE-6BE2-4BE1-97E0-6D98CAEE5687 at donders.ru.nl>
Content-Type: text/plain; charset="utf-8"
Hi Paolo,
ft_read_mri is just a generic function that reads in volumetrically represented data that comes off an mri machine. It does not care about the acquisition parameters.
Best wishes,
Jan-Mathijs
On 26 May 2019, at 15:46, Paolo Belardinelli <paolo.belardinelli at gmail.com<mailto:paolo.belardinelli at gmail.com>> wrote:
Dear FieldTrippers,
is there a way to process simultaneously T1w and T2w MR images in Fieldtrip (in line with the mri2mesh function of SimNibs)? To my understanding this is currently not possible with ft_read_mri. Am I wrong?
Best,
Paolo Belardinelli
--
--
Paolo Belardinelli, PhD
Neurology Department
University Hospital Tuebingen
Eberhard Karls University Tuebingen
Hoppe-Seyler Str. 3
D-72076 Tuebingen
Tel: +49 7071 / 29 80478
_______________________________________________
fieldtrip mailing list
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https://doi.org/10.1371/journal.pcbi.1002202
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Message: 3
Date: Sun, 26 May 2019 17:49:43 +0200
From: Paolo Belardinelli <paolo.belardinelli at gmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Processing T1 and T2 weighted MR images with
Fieldtrip
Message-ID:
<CAMa54+M4E4EPP2-v_ns=q3=BEiLE0AwzVneN4o_jks-b9g++aA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Jan.
thank you for your answer.
We acquired both T1w and T2w images.
There is no way of taking advantage of both, in the making of the sourcemodel mesh along the fiieldtrip pipeline, right?
https://protect2.fireeye.com/url?k=b58419b4-e9163bdc-b5845775-0cc47aab5830-20bd05c5d7adbf5e&q=1&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F
Best wishes,
Paolo
On Sun, May 26, 2019 at 5:35 PM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote:
> Hi Paolo,
>
> ft_read_mri is just a generic function that reads in volumetrically
> represented data that comes off an mri machine. It does not care about
> the acquisition parameters.
>
> Best wishes,
> Jan-Mathijs
>
> On 26 May 2019, at 15:46, Paolo Belardinelli
> <paolo.belardinelli at gmail.com>
> wrote:
>
> Dear FieldTrippers,
> is there a way to process simultaneously T1w and T2w MR images in
> Fieldtrip (in line with the mri2mesh function of SimNibs)? To my
> understanding this is currently not possible with ft_read_mri. Am I wrong?
>
> Best,
>
> Paolo Belardinelli
>
>
> --
> --
> Paolo Belardinelli, PhD
> Neurology Department
> University Hospital Tuebingen
> Eberhard Karls University Tuebingen
> Hoppe-Seyler Str. 3
> D-72076 Tuebingen
> Tel: +49 7071 / 29 80478
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
--
--
Paolo Belardinelli, PhD
Neurology Department
University Hospital Tuebingen
Eberhard Karls University Tuebingen
Hoppe-Seyler Str. 3
D-72076 Tuebingen
Tel: +49 7071 / 29 80478
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Message: 4
Date: Mon, 27 May 2019 06:53:02 +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] Processing T1 and T2 weighted MR images with
Fieldtrip
Message-ID: <C75ACE32-E20A-4117-9CBC-04655E4FFF51 at donders.ru.nl>
Content-Type: text/plain; charset="utf-8"
Dear Paolo,
As you know, FieldTrip relies on external packages (e.g. freesurfer and spm) for structural image processing. I suggest you look there for examples of how to incorporate T2 images to improve skull segmentation. We are looking forward to a tutorial document that describes such pipeline for Fieldtrip users. This can be submitted as a Pull Request on the website github repository: https://protect2.fireeye.com/url?k=b882c163-e410e30b-b8828fa2-0cc47aab5830-492c10c97066839d&q=1&u=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Fwebsite.
Best wishes,
Jan-Mathijs
On 26 May 2019, at 17:49, Paolo Belardinelli <paolo.belardinelli at gmail.com<mailto:paolo.belardinelli at gmail.com>> wrote:
Hi Jan.
thank you for your answer.
We acquired both T1w and T2w images.
There is no way of taking advantage of both, in the making of the sourcemodel mesh along the fiieldtrip pipeline, right?
https://protect2.fireeye.com/url?k=3a675866-66f57a0e-3a6716a7-0cc47aab5830-d6dd85a37927b5a7&q=1&u=http%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsourcemodel%2F
Best wishes,
Paolo
On Sun, May 26, 2019 at 5:35 PM Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:
Hi Paolo,
ft_read_mri is just a generic function that reads in volumetrically represented data that comes off an mri machine. It does not care about the acquisition parameters.
Best wishes,
Jan-Mathijs
On 26 May 2019, at 15:46, Paolo Belardinelli <paolo.belardinelli at gmail.com<mailto:paolo.belardinelli at gmail.com>> wrote:
Dear FieldTrippers,
is there a way to process simultaneously T1w and T2w MR images in Fieldtrip (in line with the mri2mesh function of SimNibs)? To my understanding this is currently not possible with ft_read_mri. Am I wrong?
Best,
Paolo Belardinelli
--
--
Paolo Belardinelli, PhD
Neurology Department
University Hospital Tuebingen
Eberhard Karls University Tuebingen
Hoppe-Seyler Str. 3
D-72076 Tuebingen
Tel: +49 7071 / 29 80478
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
--
--
Paolo Belardinelli, PhD
Neurology Department
University Hospital Tuebingen
Eberhard Karls University Tuebingen
Hoppe-Seyler Str. 3
D-72076 Tuebingen
Tel: +49 7071 / 29 80478
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
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