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Subject:

Re: Accidentally restarted DARTEL custom template creation and aborted miday --> ok to use for VBM8?

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Mon, 18 Jul 2016 11:23:56 +0100

Content-Type:

text/plain

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Hi Andrea,

I am not completely sure about that, but it should be ok to proceed with the given files. There should be a clear improvement visible from Template_1 to Template_6 because spatial resolution and deformation parameters are adapted to get a more crisp template image at the final end. If this is not the case and Template_1 looks as crisp as Template_6 then the displacement fields (u_rp1) were used from the previous Dartel template creation. Then you have to delete the u_rp1 images first and then rerun template creation again. Template_1 is the average after a rough initial deformation and should look much smoother then the final Template_6 image.

Best,

Christian

On Sun, 17 Jul 2016 13:38:56 +0100, Andrea Gold <[log in to unmask]> wrote:

>Hi Christian and SPM list,
>
>I am trying to create a custom DARTEL template of my 151 child participants for my VBM8 analysis. I used Batch > SPM→ Tools → DARTEL Tools → Run DARTEL (create Templates). Unfortunately, my connection was slow and I accidentially hit the "play" button on the batch screen twice. 
>
>So, it completed the first job and the Matlab window stated:
>"Done 'Run DARTEL (create Templates)' 
>Done
>
>However, then it restarted the template creation. I checked the timestamps on my files (using ls -ltr in my directory) and Template_6.nii was last written  Jul 17 07:49, then Template_0.nii, followed by a bunch of "u_rp1*" files, then Template_1.nii and the remaining "u_rp1*" files. SPM was running the 2nd iteration of cycling through the 151 subjects in the Matlab window.
>
>My question: is it (a) OK to specify Template_1 for my VBM8 analysis, given that it ran all the way through the first time and Template_6 was not touched yet, or 
>(b) is this a problem for VBM given that I stopped it partway through accidentially re-running the template creation (and it was midway through Template_1)?
>
>Thank you!
>Andrea
>
>
>>Dear Zoe,
>
>On Mon, 2 Jul 2012 16:20:20 +0000, Hyde, Zoe <[log in to unmask]> wrote:
>
>>Dear SPMers,
>> I have a question for you about the VBM8 analysis I am currently running. I used DARTEL to create a custom template from my 89 child participants. I am now going to use this custom template in the VBM8 step of 'Estimate and Write' (as I understand from the VBM8 manual that this is the recommended method when using VBM8 with a large scale paediatric sample). The DARTEL Template creation step has outputted 7 custom templates (0-6) of increasing accuracy, and Template 6 is the most accurate as it was created last and looks the crispest. However the default DARTEL template that VBM8 uses for spatial normalisation is Template 1. This is what is on line 66 of the 'cg_vbm_defaults' script in the vbm8 toolbox: vbm8.extopts.darteltpm   = {fullfile(spm('dir'),'toolbox','vbm8',' Template_1_IXI550_MNI152.nii')}; % Indicate first Dartel template. Why isn't the most accurate Template 6 used as the default template? Although Template 1 is the first template VBM8 uses, does the function then progressively go through all the templates (1-6) which have the same filename in an iterative manner?
>
>Your last assumption is correct. All templates from iteration 1-6 are used, but only the first template is defined in the defaults file. I have used the naming convention of the DARTEL toolbox.
>
>Best,
>
>Christian
>
>________________________________________
>
>Christian Gaser, Ph.D.
>Departments of Psychiatry and Neurology
>Friedrich-Schiller-University of Jena
>Jahnstrasse 3, D-07743 Jena, Germany
>Tel: ++49-3641-934752	Fax:   ++49-3641-934755
>e-mail: [log in to unmask]
>http://dbm.neuro.uni-jena.de
> 
>>Thanks a lot for your help!
>>
>>Zoe Hyde
>>Research Assistant
>>
>>Developmental Risk and Resilience Unit
>>Clinical, Educational and Health Psychology
>>Division of Psychology and Language Sciences
>>
>>University College London
>>26 Bedford Way
>>London WC1H 0AP
>>
>>[log in to unmask]<mailto:[log in to unmask]>
>>Tel: +44(0)20 7679 5322<tel:%2B44%280%2920%207679%205322> (internal: 25322)
>>http://www.drru-research.org/
>>
>>

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