Dear Matthieu,
On 9 Nov 2016, at 11:23, Matthieu Vanhoutte wrote:
> Dear Christian,
>
> 2016-11-09 11:13 GMT+01:00 Christian Gaser
> <[log in to unmask]>:
>
>> 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.
>
> I replaced all "." by "_" in the filename. I tested "resample & smooth
> surface data" and the resulting file is
> "s15mm.lh.thickness.resampled.T1_LAS_$subject.gii"
> with gifti extension. From this and under freeview this file is seen
> as a
> surface and not as overlay (as native space
> "lh.thickness.T1_LAS_$subject"
> with no ".gii" extension). How could I obtain resampled surface
> thickness
> as an overlay ".mgh" file from Freesurfer point of view ?
With CAT it’s not possible to create mgh-files. The resampled gifti
files in CAT contain the mesh structure as well as the texture
information, but Freeview is not supporting that and cannot overlay the
texture information.
However, if you want to compare Freesurfer and CAT resampled data you
can use the CAT function for resampling and smoothing Freesurfer data in
the batch editor:
SPM->Tools->CAT12-> Surface Tools->Resample & Smooth Existing Freesurfer
Thickness Data
These data can then be displayed using the CAT12 display tool. The other
way of displaying CAT-resampled data with Freeview will not work.
Best,
Christian
>
> Best,
> Matthieu
>
> P.S. : Thank you in advance for the next release solving this problem
>
>>
>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>
>>
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