Dear Christian,
I understand your doubt about studying so young subjects.
Actually, because of all the problems that you listed, it's not possible to analyze all the data togheter and I was thinking of acting like you suggested by sub-dividing them into smaller groups and by using customized templates in the age range of those sub-groups.
Because the most of subjects were acquired at an age between 5 and 18 I'll try to use TOM atlases and I'll keep those too young in stand by, unless Marko Wilke has useful advice on the processing of children less 2 years.
Thank you for support
Best regards
Elisa
>> - I'm trying both on healthy subjects and on a population
>> characterized by a disease, in this case when necessary we alreday
>> masked alterations to avoid segmentation problems.
>> In both cases we have a wide age range, from 7 months to 14-17 years
>> and we're using TPM different by TOMs to cover also the youngest ages
>> not included in TOM.
>The TOM toolbox only supports ages from 5-18 years and these data should
>also work with CAT12 without any larger issues. However, children data
>younger than 2 years will be difficult or impossible to process with
>CAT12 even if you have customized TPMs or templates. The changes due to
>development and the differences to adult brains are simply too large and
>registration and segmentation will usually fail. If you have even
>younger subjects the intensities in the T1 image are also affected
>(inverse) and only customized software can deal with these data.
>
>Moreover, it will be difficult at all to process and more important to
>analyze data in that large age range because the changes due to
>development will be huge. This will be a general issue if you include
>subjects younger than 2-5 years (difficult to define a cutoff) because
>it will be difficult or not meaningful to create a template that fits to
>all data. If you use different templates you will have a bias due the
>template selection and cannot analyze the data together.
>
>However, if you don’t want to analyze all data together this will be
>easier to handle and you can use the same customized template for a
>certain age range. Again, you have to think about excluding the subjects
>which are too young because of processing issues.
>
>Maybe Marko Wilke can also comment because he has more experience with
>children data and has maybe already tried to process data < 2 years of
>age.
>
>Best,
>
>Christian
>
>
>>
>> - I've already reset the origin in AC both in TPMs and our images to
>> minimize realignment errors.
>> I was wondering if using different options of affine regularization as
>> the "average size template" instead of the default "ICBM space
>> template", may influence the results about surface.
>>
>> Otherwise, since my aim is to obtain values in some specific areas, is
>> it possible to bypass the default internal atlas, generate surfaces
>> for the whole brain without separating the two hemispheres and then
>> use ad hoc templates, in the same space of TPMs, to separate the two
>> hemispheres and to extract values only from the regions of interest?
>>
>> Thank you
>> Elisa
>>
>> On Wed, 9 Nov 2016 09:45:56 +0000, Christian Gaser
>> <[log in to unmask]> wrote:
>>
>>> Dear Elisa,
>>>
>>> On Tue, 8 Nov 2016 10:27:33 +0000, Elisa Marchetta
>>> <[log in to unmask]> wrote:
>>>
>>>> Dear CAT experts,
>>>>
>>>> I started using CAT12 to calculate cortical thickness and sulcal
>>>> depth.
>>>>
>>>> After some tests on adults' T1 images, I've started using it on
>>>> pediatric population. To have a more accurate segmentation I changed
>>>> the default TPM with specific pediatric TPM of corresponding age.
>>>
>>> Here I need more information: What type of pediatric population (age,
>>> any diseases?) and what kind of specific TPM have you used (using TOM
>>> toolbox, or any other TPM)?
>>>
>>>> The segmentation works perfectly and in many cases the surface
>>>> calculation too.
>>>>
>>>> Unfortunately in many other cases, during the surface calculation,
>>>> something goes wrong and in the results the two hemispheres are
>>>> badly recognized, with the left hemisphere taking into account also
>>>> a great portion of the right one and the right hemisphere cut in a
>>>> bad way.
>>>
>>> CAT12 uses an internal atlas to divide the hemispheres and to fill
>>> subcortical structures and ventricles. If your pediatric data deviate
>>> too much this internal atlas might not fit very well. However, the
>>> issues could be also caused by realignment errors. Please can you try
>>> to set the AC first and run the preprocessing again for a few
>>> selected subjects, where these issue occured.
>>>
>>> Best,
>>>
>>> Christian
>>>
>>>>
>>>> I guess the problem is related with age, but sometimes subjects with
>>>> the same age and similar images have very different results.
>>>>
>>>> Do you have an idea on how can I solve this problem?
>>>>
>>>> I thank you in advance for any advice about it
>>>> Best regards
>>>> Elisa
>>
|