[FieldTrip] segmented brain seems not fitting the sensor helmet well

[Lilla.Magyari at mpi.nl]

hi Ye,

here is a FAQ about the function of the ft_volumereslice function:
http://fieldtrip.fcdonders.nl/faq/how_change_mri_orientation_size_fov

One of the reasons why it is suggested to use the ft_volumereslice
function before segmentation is that some of the segmentation-processes
require isotropic voxels (this means that a voxel must have the same size
into each direction). The ft_volumereslice function is reslicing the image
and returns it with isotropic voxel-size. But if your mri images are
isotropic, you do not need to bother with this.

But you have to be careful when you use the ft_volumereslice function and
you do not specify the resolution or the dimensions of its output. In this
case, it will return the image resliced to a default resolution and a
default dimension (it is 256X256X256 with 1 mm resolution if I remember
well), and it is possible that your image will loose some information. I
suspect that this happened when you resliced your mri. Can you see the
whole brain when you plot the resliced mri with the ft_sourcplot function?
The solution for this problem is that you define the resolution and the
dimensions yourself for ft_volumereslice.

I hope this helps.

Best,
Lilla




> Hello All,
>
> I found the problem I mentioned in the previous email was caused by
> using "mri_sliced = ft_volumereslice([], mri);" before using
> ft_volumesegment.
> After erasing the line "mri_sliced = ft_volumereslice([], mri);", the
> segmented brain seems to be normal and fits the sensor helmet well now,
> as show in the attached figure(notvolumnsliced.jpg).
> For another of my subject, if the "ft_volumereslice" is included, the
> brain looks sliced on the top(subject2vs.jpg). If no "ft_volumreslice"
> it looks normal(subject2.jpg).
>
> I notice in the fieldtrip headmodel tutorial
> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg),
> "ft_volumereslice" is not used. but in the field trip beamformer
> tutorial(http://fieldtrip.fcdonders.nl/tutorial/beamformer), it is used.
>
> I am wondering if I should include "ft_volumereslice" in my source
> localization code. Can anyone give me some suggestions?
>
>
>
> thanks ahead,
> Ye
>
>
>
>
> On 13-02-28 11:45 AM, fieldtrip-request at science.ru.nl wrote:
>> Send fieldtrip mailing list submissions to
>> 	fieldtrip at science.ru.nl
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 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. segmented brain seems not fitting the sensor helmet well (Ye Mei)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 28 Feb 2013 11:38:21 -0500
>> From: Ye Mei <frank.ye.mei at gmail.com>
>> To: fieldtrip at science.ru.nl
>> Subject: [FieldTrip] segmented brain seems not fitting the sensor
>> 	helmet well
>> Message-ID: <512F87FD.80500 at gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>>
>> Hello FieldtripList,
>>
>> After segmentation and alignment using
>> 'ft_volumesegment' and 'ft_volumerealign', one of the subjects'
>> segmented
>> brain seems rotated forward in the sensor helmet(brain.png) and the
>> cerebellum part seems to be segmented out. However, his head MRI seems
>> fitting the sensor helmet well(head.jpg). My another subject's brain
>> seem to be correctly segmented without missing the cerebellum part. And
>> the brain is not rotated forward.
>>
>> Could might be the problem?
>>
>> thanks ahead,
>> Ye
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: brain.png
>> Type: image/png
>> Size: 15197 bytes
>> Desc: not available
>> URL:
>> <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/1d01f497/attachment.png>
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: head.jpg
>> Type: image/jpeg
>> Size: 50294 bytes
>> Desc: not available
>> URL:
>> <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/1d01f497/attachment.jpg>
>>
>> ------------------------------
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> End of fieldtrip Digest, Vol 27, Issue 31
>> *****************************************
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip