[FieldTrip] holes in head

[Cristiano Micheli]

Hi Maris,
it's interesting. I think there is no need (for now) to upload the data
though. Could you attach the code that you used to generate the figures?
There might be important information there, such as the coordinate system
or the resolution of the MR scans (what is the FOV? What is the slice
distance? etc...)

It'd be great if you could patch the snippet of code.

All the best!
Cris



On Mon, Aug 17, 2015 at 2:51 PM, Maris Skujevskis <icelandhouse at gmail.com>
wrote:

> Thanks for your suggestion, Cristiano. However, the anatomical images do
> cover the entire head!
>
> There seem to be two possibilities - either there is something wrong in
> how some lower level function employed by ft_volumerealign creates the head
> surface out of my MR files or there are some real deformities present in my
> MR images.
>
> Since I do not have a well-trained eye for this, could someone take a
> quick look at a couple of the original MR files of any of these subjects
> (same link as previously): https://goo.gl/photos/txeai9EfFXCn4hQ17 and
> say whether they look distorted in any way? Let me know and I will share
> the MR files.
>
> Best wishes,
> Maris
>
>
>> Date: Mon, 17 Aug 2015 11:46:38 +0200
>> From: Cristiano Micheli <michelic72 at gmail.com>
>> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
>> Subject: Re: [FieldTrip] holes in head
>> Message-ID:
>>         <CADW7XCD_78QQBAj1WvM=
>> ZT2mdpTxePPwDT72z1hU9biQ7--ipA at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>>
>> Dear Maris
>>
>> I am heavily guessing here, but are the anatomical MRI images cut on top?
>> I
>> only encountered this in the case that the MRI slices covered an
>> incomplete
>> volume of the head.
>>
>> It might be something else, though this is easy to check...
>>
>> Good luck
>> Cris
>>
>>
>> On Sat, Aug 15, 2015 at 7:02 PM, Maris Skujevskis <icelandhouse at gmail.com
>> >
>> wrote:
>>
>> > Dear Fieldtrip community,
>> >
>> > When plotting the head shape with ft_volumerealign (the input to the
>> > ft_volumerealign function being simpy the output produced by the
>> > ft_read_mri), some of the subjects show deep crater-like holes in the
>> head
>> > surface.
>> > Images available here: https://goo.gl/photos/txeai9EfFXCn4hQ17
>> >
>> > Does anyone have an idea what might have caused these 'holes'?
>> >
>> > If this is incomplete information to be able to answer the question,
>> > please ask so I can provide further details.
>> >
>> > Best wishes,
>> > Maris
>> >
>> >
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