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!
>>
>>
>