Dear all,
Looking at the intersection of the analysis mask (mask.nii) and the mask
of interest is probably the best way to proceed. Entering a value of 1
when asked for height threshold (after selecting 'none') will actually
correspond to p<1 (see the inequality at line 729 in spm_getSPM.m) which
will correspond to a threshold of -Inf for a T-statistic and 0 for an
F-statistic. Assuming an extent threshold of 0 is chosen, all voxels
should then appear in the MIP.
Best regards,
Guillaume.
On 03/12/16 12:25, Torben Lund wrote:
> Dear Rachel
>
> Entering a p-value of 1.00 will actually be interpreted (by SPM) as a t or F value of 1.
>
>
> Best
> Torben
>
>
>> On 2 Dec 2016, at 15.58, Colin Hawco <[log in to unmask]> wrote:
>>
>> Alternately, you Can use the function spm_mask to apply a mask to a t-map, and use an external viewer such as MRIcron to view your t-maps overlaid on an anatomical image.
>>
>> Colin Hawco, PhD
>> Neuranalysis Consulting
>> Neuroimaging analysis and consultation
>> www.neuranalysis.com
>> [log in to unmask]
>>
>>
>>
>> -----Original Message-----
>> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Marko Wilke
>> Sent: December-02-16 2:02 AM
>> To: [log in to unmask]
>> Subject: Re: [SPM] SPM threshold while masking question
>>
>> Rachel,
>>
>> if you only look at the results, you may not see all voxels as some thresholding is done beforehand. You may want to look at the mask.img image in your stats folder to see which voxels were included in the first place. To mend this, you would have to play with the masking options in the statistical setup.
>>
>> Cheers
>> Marko
>>
>> Lepage, Rachel wrote:
>>> Hello all,
>>>
>>> I am trying to figure out how to view all active voxels within a mask
>>> (at p=1.0). When viewing t-test results, I am placing a mask on and
>>> setting the p-value as p = 1.0; therefore, all voxels within the mask
>>> should appear. However, only small clusters within the mask are
>>> showing voxel activation in the SPM output, even at p = 1.0. Would
>>> anyone know a way to view all voxel activation within a mask? (Using
>>> SPM8 currently)
>>>
>>> Thanks so much,
>>>
>>> Rachel
>>>
>>> *Rachel LePage, BS*
>>> /Research Associate,/ Psychiatry
>>>
>>> Western Psychiatric Institute and Clinic *[log in to unmask]
>>> <mailto:[log in to unmask]>*
>>>
>>> _cid:image001.png@01D1AF95.1368ACB0
>>>
>>> _
>>>
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>>
>> --
>> ____________________________________________________
>> Prof. Dr. med. Marko Wilke
>> Facharzt für Kinder- und Jugendmedizin
>> Leiter, Experimentelle Pädiatrische Neurobildgebung
>> Universitäts-Kinderklinik
>> Abt. III (Neuropädiatrie)
>>
>> Marko Wilke, MD, PhD
>> Pediatrician
>> Head, Experimental Pediatric Neuroimaging
>> University Children's Hospital
>> Dept. III (Pediatric Neurology)
>>
>> Hoppe-Seyler-Str. 1
>> D - 72076 Tübingen, Germany
>> Tel. +49 7071 29-83416
>> Fax +49 7071 29-5473
>> [log in to unmask]
>>
>> http://www.medizin.uni-tuebingen.de/kinder/epn/
>> ____________________________________________________
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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