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Subject:

Re: CAT12 - Mask for Surface based morphometry results?

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Thu, 6 Apr 2017 16:08:09 +0200

Content-Type:

text/plain

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text/plain (248 lines)

Dear Robin,


On 6 Apr 2017, at 15:27, Robin Shao wrote:

> Dear Prof. Gaser,
>
>
> Many thanks again for your patient reply. I think my confusion stems 
> from a rather basic point--so in the case of VBM, even if I normalized 
> my customized DARTEL template by running "population to ICBM 
> registration', data in this customized-DARTEL-normalized space still 
> do not match well with the default DARTEL volume atlas maps (e.g. 
> DARTEL IXI template), despite that both should be in the MNI space 
> (rather than one in the customized DARTEL space and the other in the 
> default DARTEL space)? Or have I got it wrong?

The “population to ICBM registration“ will end up in a more or less 
different space than the DARTEL IXI space from CAT12. The crucial point 
is that the mapping from 3D to surface will be very sensitive for any 
discrepancies because this mapping will use the intersection between 
surface and 3D image and will map inside the cortical band. However, if 
the 3D image is differing from the surface this will not work.

Best,

Christian

>
>
> Thanks again for the help.
>
>
> Robin
>
>
> Sent from Outlook<http://aka.ms/weboutlook>
>
>
> ________________________________
> From: Christian Gaser <[log in to unmask]>
> Sent: Thursday, April 6, 2017 1:47 PM
> To: [log in to unmask]; [log in to unmask]
> Cc: Christian Gaser
> Subject: Re: CAT12 - Mask for Surface based morphometry results?
>
> Dear Robin,
>
> On Sun, 26 Mar 2017 19:53:29 +0000, Robin Shao <[log in to unmask]> 
> wrote:
>
>> Dear Prof. Gaser,
>
>> Many thanks for your detailed explanation. I think I understand it 
>> now...
>
>> Does it then mean that even with a customized-DARTEL-template 
>> approach, one can still (sort of) perform ROI-based analysis on SBM 
>> results, >provided the ROIs are generated from some other analysis, 
>> such as VBM analysis on the same data set, ultilising the methods 
>> below? I know >that more classic atlas-based ROI approach is not 
>> applicable for VBM or SBM analysis using customized DARTEL templates. 
>> If so I have a few >further questions:
>
> Because the surface registration is completely independent from the 3D 
> (Dartel) registration you can use surface ROIs even for data where you 
> have created a customized template. However, for any volume based 
> atlases this will not work properly because of the discrepancy between 
> your customized Dartel space and your ROI space.
>
>> 1) Can I extract surface-based measures such as cortical thickness 
>> using the mapped mask?
>
> The mapping is done using the DARTEL IXI template provided with CAT12 
> and if you map data from any other space to the surface this will be 
> not precise enough.
>
>> 2) If I have anatomical labels for the original mask based on VBM 
>> analysis, would the same label apply for the surface-based analysis 
>> after the >mask is applied to the surface? I guess probably not as 
>> VBM and SBM use different atlas system.  If so, what would be the 
>> best way to know the >new label of this mask on surface?
>
> To be honest I don't know...
>
>> 3) May I just confirm that with SBM using customized DARTEL template 
>> (during segmentation), can I still use the two atlases provided by 
>> CAT12 >to get the anatomical labels? Actually, I read from previous 
>> mail that customized DARTEL has very little impact on the SBM 
>> results. Does that >mean that one can refrain from using customized 
>> DARTEL, even for pediatric samples?
>
> Yes, you can use these ROIs, see my answer above. This should probably 
> also work for pediatric data because the sulcal and gyral patterns 
> will be used for registration and these patterns should be consistent 
> even for pediatric data (sure for age >1-2 years, all below this age 
> will be difficult).
>
> Maybe, you think too complicated and should simply use some predefined 
> ROIs for masking your results...
>
> Best,
>
> Christian
>
>> I apologize for the flood of questions...
>
>
>
>> Best regards,
>> Robin
>
>> Sent from Outlook
>
>
> From: Christian Gaser <[log in to unmask]>
> Sent: Sunday, March 26, 2017 8:37 PM
> To: Robin Shao
> Cc: [log in to unmask]
> Subject: Re: CAT12 - Mask for Surface based morphometry results?
>
> Dear Robin,
> if you map a native image to it’s native surface this is done before 
> spherical registration. If you map normalized volumes to the template 
> surface, the latter is the template for the spherical registration. As 
> surface for the mapping (and only for the mapping!) I don’t use the 
> fsaverage surface from freesurfer, but the extracted surface of the 
> Dartel MNI template (which is used for volume normalization as 
> template) which was spherically registered to the fsaverage template. 
> Therefore this surface corresponds to both the surface- and the 
> volume-based registration space. Sounds complicated, but works…
> Best,
> Christian
> Christian Gaser, Ph.D.
> Professor of Computational Neuroscience/Neuroimaging
> Biomagnetic Center
> Structural Brain Mapping Group
> Department of Neurology
> Jena University Hospital
> Am Klinikum 1, D-07747 Jena, Germany
> Tel: ++49-3641-9325778 Fax: ++49-3641-9325772
> e-mail: [log in to unmask]
> http://www.neuro.uni-jena.de
> On 26 Mar 2017, at 21:23, Robin Shao wrote:
> Dear Dr. Gaser,
>
> Thanks for your reply. In that case, why can the mapped 3D data be 
> applied directly onto the result maps of surface-based analysis, given 
> the latter were spherical registered?
>
> I apologize if I have greatly misunderstood your words.
>
> Thanks again.
>
> Robin
>
> Sent from Outlook
>
>
> From: Christian Gaser <[log in to unmask]>
> Sent: Sunday, March 26, 2017 8:18 PM
> To: [log in to unmask]; [log in to unmask]
> Cc: Christian Gaser
> Subject: Re: CAT12 - Mask for Surface based morphometry results?
>
> Dear Robin,
>
> the mapping of spatially normalized 3D data (in Dartel MNI space) is 
> using a surface that was extracted from the Dartel template (without 
> spherical registration).
>
> Best,
>
> Christian
>
> On Sun, 26 Mar 2017 18:54:33 +0000, Robin Shao <[log in to unmask]> 
> wrote:
>
>> Dear all,
>>
>>
>> May I ask whether the mapping function works if both volume- and 
>> surface-based data were obtained using segmentation based on 
>> customized DARTEL template? I thought not as I believe the spherical 
>> registration of surface data were based on some default DARTEL map, 
>> not customized ones?
>>
>>
>> Many thanks,
>>
>> Robin
>>
>>
>> Sent from Outlook<http://aka.ms/weboutlook>
>>
>>
>> ________________________________
>> From: SPM (Statistical Parametric Mapping) <[log in to unmask]> on 
>> behalf of Rodolphe Nenert <[log in to unmask]>
>> Sent: Friday, March 24, 2017 5:08 PM
>> To: [log in to unmask]
>> Subject: Re: [SPM] CAT12 - Mask for Surface based morphometry 
>> results?
>>
>> Thanks a lot for your advice Christian, it worked perfectly!
>>
>> Allow me a follow-up question, is it still possible to use the T-to-p 
>> map tool as I can�t use combine spmT files with my mask with a tool 
>> like imcalc. ?
>>
>> Thanks again,
>>
>> Rodolphe.
>>
>>> On Mar 24, 2017, at 2:52 AM, Christian Gaser 
>>> <[log in to unmask]> wrote:
>>>
>>> Dear Rodolphe,
>>>
>>> On Thu, 23 Mar 2017 09:58:28 -0500, Rodolphe Nenert 
>>> <[log in to unmask]> wrote:
>>>
>>>> Basically, I want to use an exclusive mask to create a contrast 
>>>> result following a SBM analysis.
>>>>
>>>> 1) CAT12 tool to create p-maps from T-maps does not seem to have 
>>>> the masking option. Is there another way to do it?
>>>>
>>>> 2) As the second level analysis is done with SPM12, I could 
>>>> eventually create the contrast in SPM and use the masking option, 
>>>> but my mask is a nifti file. Is there a way to convert my .nii file 
>>>> into .gii file for that particular purpose?
>>>>
>>> You can use the mapping function "Map Normalized Volume (Template 
>>> Space) to Template Surface" to map nifti-data to a surface. Please 
>>> note that the nifti image has to be in the template space (Dartel 
>>> MNI after CAT12 spatial registration). Then you can use this mapped 
>>> mask image as exclusive mask in the SPM results section.
>>>
>>> Best,
>>>
>>> Christian
>>>
>>>> Thanks!
>>>
>>>
>>

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