Dear Andre,
you have to copy the files in a folder spm12/atlas but you have to
create it first:
mkdir(spm('Dir'),'atlas');
To create a mask from a set of regions, use the spm_atlas function: you
can specify a list of labels or use regular expressions:
VM = spm_atlas('mask','AAL',{'Putamen_L'});
VM.fname = 'ROI_left_putamen.nii';
VM = spm_write_vol(VM,VM.dat);
As for the F-contrast to use for specifying effects of interest, you
probably want to use [1 0;0 1].
Best regards,
Guillaume.
On 14/04/15 16:53, André Schmidt wrote:
> Dear list,
>
> I want do the same - in which folder exactly do I have to copy the AAL.nii and AAL.xml?
>
> Furthermore, I intend to use the AAL to create some ROIs - how can I do that in SPM12?
>
> Finally, I like to run a DCM analysis. I have already created a design matrix with two regressors, the first includes all trial s(input) and the second the modulator. Is it ok to extract time series from my ROIs with a -1 1; 1 -1 F contrast (with adjustment for this contrast)?
>
> Many thanks for your help
> Andre
>
>
> ________________________________________
> Von: SPM (Statistical Parametric Mapping) [[log in to unmask]]" im Auftrag von "Guillaume Flandin [[log in to unmask]]
> Gesendet: Montag, 13. April 2015 20:23
> An: [log in to unmask]
> Betreff: [SPM]
>
> Dear Negar,
>
> which version of SPM are you using?
>
> In SPM12, you can label peaks and clusters in MNI space by selecting:
> Atlas > Label using > Neuromorphometrics
> from the Results section: labels will be available from right click on
> peak coordinates and cluster size.
> If you want to use labels provided by the AAL atlas, download it from here:
> http://www.gin.cnrs.fr/AAL/aal_for_SPM12.tar.gz
> and copy files AAL.nii and AAL.xml in a folder called 'atlas' in your
> SPM installation. The "AAL" option will then appear in the menu
> described above (after restarting SPM).
>
> Best regards,
> Guillaume.
>
>
> On 13/04/15 08:24, Negar Chabi wrote:
>> Dear All.
>>
>> I have been using AAL to define the name of activated region.
>> At first I faced with the following error:
>> ??? Error using ==> spm_P
>> Too many output arguments.
>> Error in ==> gin_clusters_plabels at 251
>> [P Pn Em En EN] = spm_P(1,k,u,df,STAT,R,n,S);
>> Error in ==> gin_clusters at 20
>> gin_clusters_plabels('List',xSPM);
>> ??? Error while evaluating uicontrol Callback
>>
>> when I checked the emails I resolved it by replacing [P Pn Em En] =
>> spm_P(1,k,u,df,STAT,R,n,S); rather than [P Pn Em En EN] =
>> spm_P(1,k,u,df,STAT,R,n,S);
>>
>> But after that I faced with this waring :
>> Warning : No voxels survive height threshold at u =15;
>>> In spm_getSPM at 768
>> In ne
>>
>> I don't know why this warning happens and how to resolve it.
>>
>> Any suggestions will be greatly appreciated.
>>
>> Best.
>>
>>
>>
>> --
>> Negar Chabi
>> Msc of medical engineering
>> Persian Gulf Nuclear Medicine Research Center
>> Bushehr University of Medical sciences
>
> --
> Guillaume Flandin, PhD
> Wellcome Trust Centre for Neuroimaging
> University College London
> 12 Queen Square
> London WC1N 3BG
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
|