Thank you Guillaume, I will try this.
Meanwhile would you mind explaining the 'topological interference' thing
for me? Is it a problem to go by e.g. p<0.01; 3500 voxel cluster
threshold and p<0.05 FWE cluster correction?
Cheers,
Barbara
On 19/05/2017 16:08, Guillaume Flandin wrote:
> Dear Barbara,
>
> Why not using the higher level module from the batch interface:
> SPM > Stats > Results Report
> There you can save the thresholded map as a NIfTI image, as well as the
> results table in CSV or Excel format. This can take place without any
> interaction and without graphical display if you set the defaults
> accordingly:
> spm_get_defaults('cmdline',true);
> After the execution of the job, the TabDat variable is also available in
> the MATLAB workspace, allowing you to access the same information than
> the one you got so far, e.g. TabDat.dat{1,3}.
> Note that for topological inference in SPM, the cluster forming
> threshold should not be set lower than p<0.001 uncorrected.
>
> Best regards,
> Guillaume.
>
>
> On 19/05/17 15:00, Barbara Kreilkamp wrote:
>> Dear Rouhi,
>>
>> Thank you very much, this seems to work quite well. However, I'd like to
>> avoid the interactive thing, because I have quite a few clusters to
>> extract, all at p<0.01 and a specific voxel cluster threshold.
>>
>> Is there an SPM function that does not do this interactively or do I
>> have to reprogram myself?
>>
>> This is what I've got so far:
>>
>> [hReg,xSPM,SPM]=spm_results_ui % just to get hReg and xSPM for spm_list
>> - but too interactive
>>
>> spm_list('ListCluster',xSPM,hReg,[1,8,'ALLORNOTHING'])
>> ans.dat{1,3}
>>
>>
>> Thanks,
>> Barbara
>>
>>
>> On 19/05/2017 11:33, Rouhollah Abdollahi wrote:
>>> Dear Barbara,
>>>
>>> Try spm_list() function.
>>>
>>> Best regards
>>> Rouhi
>>>
>>> Best Regards
>>> Rouhollah Abdollahi
>>>
>>> *Institut für Neurowissenschaften und Medizin (INM-3)*
>>> Forschungszentrum Jülich
>>> Leo-Brandt-Straße
>>> 52425 Jülich, Germany
>>>
>>> Tel: +49 2461 61-4686
>>>
>>>
>>>
>>>
>>> On Fri, May 19, 2017 at 10:51 AM, Barbara Kreilkamp
>>> <[log in to unmask]
>>> <mailto:[log in to unmask]>> wrote:
>>>
>>> Dear all,
>>>
>>> Any hint on this is greatly appreciated.
>>>
>>> Thanks a lot,
>>>
>>> Best wishes,
>>>
>>> Barbara
>>>
>>>
>>>
>>> -------- Forwarded Message --------
>>> Subject: [SPM] extract large number of p-values from clusters
>>> Date: Tue, 16 May 2017 14:52:40 +0200
>>> From: Barbara Kreilkamp <[log in to unmask]>
>>> <mailto:[log in to unmask]>
>>> To: [log in to unmask] <mailto:[log in to unmask]>
>>>
>>>
>>>
>>> Dear SPMers,
>>>
>>> Is there a way to save multiple cluster p-values of different
>>> t-tests without continuously opening the results tab with SPM.mat?
>>>
>>> E.g. is there a procedure in SPM with which I can load the SPM
>>> file in MATLAB to extract p-values of clusters with a certain size?
>>>
>>> Thank you very much,
>>>
>>> Best wishes,
>>>
>>> Barbara
>>>
>>>
>>>
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