Dear Christian,
thank you for your quick reply.
Here the details you asked for:
- 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.
- 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
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