[FieldTrip] fieldtrip Digest, Vol 80, Issue 7

RICHARDS, JOHN RICHARDS at mailbox.sc.edu
Sun Jul 9 14:45:10 CEST 2017


The ft_volumesegment uses the SPM program that does gm/wm segmentation into probability maps.  In the case of using =  {'brain', 'skull', 'scalp'}; as input, the program sums the PVE for GM, WM and "CSF" (other matter) to create the brain (+ fill holes and some other); then has a formula for finding the skull (dilate brain, or use bone class from segmented MRI), and scalp.

So the "skullstrip" portion consists of the brain PVEs from the SPM segmentation program.  If that program does not work correctly then the overlap of the brain mask will not match the actual brain--could either not cover all the brain or cover more than the brain.

I have had some issues with the SPM algorithm, and its use in the ft_volumesegment is not very flexible.  I do the segmentation outside of FT using FSL tools (e.g., bet, bet2, betsurf) and then import the segmented head into FT format; FSL also has an algorithm for "skull stripping" found in its VBM script.  This way I have more control over the initial segmented products.  Additionally, neither the SPM nor the FSL routines work with some pediatric populations, especially infants under 2 years of age. In that case I often substitute the initial MRI template (in FT case, as SPM, they use the MNI segmented head) with an infant MRI template and get much better results.  (e.g., neurodevelopmental MRI database).  At times I have used the SPM algorithms for brain segmenting (GM, WM, CSF) and in this case also the PVEs from an age-appropriate brain improve the results.


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
HTTP: jerlab.psych.sc.edu

-----Original Message-----
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of fieldtrip-request at science.ru.nl
Sent: Sunday, July 9, 2017 6:00 AM
To: fieldtrip at science.ru.nl
Subject: fieldtrip Digest, Vol 80, Issue 7

Send fieldtrip mailing list submissions to
	fieldtrip at science.ru.nl

To subscribe or unsubscribe via the World Wide Web, visit
or, via email, send a message with subject or body 'help' to
	fieldtrip-request at science.ru.nl

You can reach the person managing the list at
	fieldtrip-owner at science.ru.nl

When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..."

Today's Topics:

   1. brain segmentation problem (Elena Orekhova)


Message: 1
Date: Sat, 8 Jul 2017 19:11:17 +0200
From: Elena Orekhova <orekhova.elena.v at gmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: [FieldTrip] brain segmentation problem
	<CAGuwe0JDC-b=_hn6_0sox9_hxA-_+edxbx4KXVG5hUQLuTD+Lg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Fieldtrip experts,

I noticed that ft_volumesegment sometimes produces inaccurate results, extending the brain mask outside the brain (see the attached figure).  I used

mri_orig= ft_read_mri ('T1.mgz');
cfg           = [];
cfg.output    =  {'brain', 'skull', 'scalp'};
mri_segmented = ft_volumesegment(cfg, mri_orig_realigned);

Have anybody had such a problem. How can it be resolved?

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170708/6bdd59e7/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: fig1.png
Type: image/png
Size: 66721 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20170708/6bdd59e7/attachment-0001.png>


fieldtrip mailing list
fieldtrip at donders.ru.nl

End of fieldtrip Digest, Vol 80, Issue 7

More information about the fieldtrip mailing list