Dear Matthieu,

On 9 Nov 2016, at 11:04, Matthieu Vanhoutte wrote:

> Dear Christian,
>
> 2016-11-09 10:50 GMT+01:00 Christian Gaser 
> <[log in to unmask]>:
>
>> 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
>>
>
> My original filename is "T1.LAS.$subject.nii". Thickness data in 
> native
> space is "lh.thickness.T1.LAS.$subject" and after resampling and 
> smooth
> "s15mm.lh.thickness.resampled.T1.LAS.$subject.gii". Which "." do I 
> have to
> replace with "_" in the filenames and which preprocessing steps do I 
> have
> to relaunch ?

Any „.“ in „T1.LAS.$subject“ should be replaced. Relaunch those 
steps where the error occurred (Display, Extract ROI-based Surface 
Values). It is not necessary to rerun CAT12 again. This error only 
affects that parts of CAT12 where a texture file such as thickness is 
used for further processing and the related surfaces (central surface) 
couldn’t be found.

Best,

Christian

>
> Best regards,
> Matthieu
>
>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>