Dear Matthieu,
On Tue, 8 Nov 2016 20:27:27 +0100, Matthieu Vanhoutte <[log in to unmask]> wrote:
>Dear experts,
>
>Does anybody have answer to my questions in last mail ?
>
>Best regards,
>Matthieu
>
>> Le 3 nov. 2016 à 16:44, Matthieu Vanhoutte <[log in to unmask]> a écrit :
>>
>> Dear CAT12's experts,
>>
>> 1) Could you precise me what is the impact of TPM maps onto central surface and surface extracted data ?
The TPM is only used for the initial registration and segmentation. Because CAT is using a segmentation approach without use of priors the impact of the TPM on the overall results will be minor, except for children data. For children data I would strongly recommend to create customized TPMs. Please also keep in mind that the surfaces are extracted using segmentations in native space without any spatial registration. However, the initial registration can also bias your final segmentation and skull-stripping...
>>
>> 2) In case of atrophied patients, wouldn't it better to create own TPM with DARTEL for surface features ? (and own customized TPM with TOM too ? )
There are different TPMs or templates used in CAT12:
TPM - used for initial registration and segmentation (followed by segmentation without use of priors)
DARTEL template - used for high-dimensional spatial registration
Freesurfer surface template - used for surface registration
Of course, a customized DARTEl template will influence the results of your spatial registration. However, the impact on surfaces will be minor, because here a surface registration is used (where no opportunity exists to create own templates). Thus, a customized DARTEL template will influence mostly your VBM data, but almost nothing your surface data (there might be some minor influence because some internal atlas maps are used to fill ventricles and subcortical areas and to divide the hemispheres).
Personally, I only create customized templates for children data, but not for atrophied brains. Of course, there are some advantages in using a customized DARTEL template for atrophied brains, but you will loose some useful features such as ROI analysis (which is DARTEL atlas based) and the ease of processing your data with an existing template and the advantages/weaks of using a customized template might also depend on your data. In case of doubts create a customized DARTEL template and compare the results to the standard template.
>>
>> 3) Finally for statistical analysis, are preprocessed surface features extracted compatible with Freesurfer's fsaverage allowing possibly to use another framework than SPM for analysis ?
The surface features such as thickness, gyrification are saved in freesurfer format and could be also used with other software. However, even if CAT12 uses some freesurfer naming conventions freesurfer is expecting certain files and folders that don't exist in CAT12.
The surface features such as thickness are estimated in native space and need to be resampled/transformed according to the fsaverage surface (after surface registration). This is done in CAT12 with the "resample & smooth surfaces" function (where the surface registration is considered) and the resampled data are finally in gifti format and could be used with any other software. This is similar to the step in freesurfer where the command "mris_preproc" is used to resample data into fsaverage space. However, the output format in freesurfer is different and all files are concatenated into a single mgh-file.
Best,
Christian
>>
>> Best regards,
>> Matthieu
>>
>>
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