Dear Matthieu,
>Ok I think I understood that the last part of my filename as an additional
>"." not supported by the actual version of CAT12, doesn't it ?
>
>How could I solve this problem temporarily while waiting for the new
>release of CAT12 ?
I hope we have the new release ready this week. Until then, you can simply replace the "." with "_". Please keep in mind that you also have to change the related files with "central" and "sphere" and "sphere.reg" in the name:
T1.LAS -> T1_LAS
Best,
Christian
On Wed, 9 Nov 2016 10:36:00 +0100, Matthieu Vanhoutte <[log in to unmask]> wrote:
>Dear Christian,
>
>See below for my question...
>
>2016-11-09 10:28 GMT+01:00 Christian Gaser <[log in to unmask]>:
>
>> Dear Matthieu,
>>
>> see below for my answer...
>>
>> On Wed, 9 Nov 2016 10:05:14 +0100, Matthieu Vanhoutte <
>> [log in to unmask]> wrote:
>>
>> >Dear Christian,
>> >
>> >Thanks for the detailed answers !
>> >
>> >Please see in-line below.
>> >
>> >Best regards,
>> >Matthieu
>> >
>> >
>> >2016-11-09 9:48 GMT+01:00 Christian Gaser <[log in to unmask]>:
>> >
>> >> 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.
>> >>
>> >
>> >I managed to open thickness in native space (without any extension file as
>> >'gii') as overlay onto the central surface within freeview. However, when
>> I
>> >tried to open resampled thickness, which has '.gii' extension, I only
>> >managed to open it as a surface on freeview and have not seen the
>> thickness
>> >values.
>> This is the issue with the additional "." in the filename which I
>> mentioned in another answer to your question. We will solve this issue...
>>
>
>Ok I think I understood that the last part of my filename as an additional
>"." not supported by the actual version of CAT12, doesn't it ?
>
>How could I solve this problem temporarily while waiting for the new
>release of CAT12 ?
>
>Best regards,
>Matthieu
>
>
>>
>> >Moreover, once load thickness resampled gifti file and fsaverage space, I
>> >could see that the the two surfaces weren't identical.
>> The freesurfer fsaverage surface is used for spatial registration and as
>> common mesh structure (tetrahedral mesh with defined number of vertices and
>> faces) for the resampled files. Of course, the shapes will be different
>> because of the different coordinates. Only the underlying mesh structure is
>> from fsaverage and should be the same. The shape is from the individual
>> data and will be different.
>>
>> Best,
>>
>> Christian
>> >
>> >Could you give me an explanation ?
>> >
>> >
>> >>
>> >> Best,
>> >>
>> >> Christian
>> >>
>> >> >>
>> >> >> Best regards,
>> >> >> Matthieu
>> >> >>
>> >> >>
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >
>>
>>
>>
>
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