Hi Xu,
there is a global variable defaults.analyze.flip, set by spm_defaults
and used by spm_vol, which affects the way analyze images are
interpreted. As far as I understand it, it is meant to be defined
once and forever for each lab, depending on if you want your images
to be flipped during normalization or not. If you directly load the
*.mat file, you are ignoring these local preferences.
regards,
Matthias Reimold
Am 22.05.2006 um 18:32 schrieb Xu Cui:
> Hi, SPMers,
>
> I am wondering if anybody knows why the coordinate conversion
> matrices in SPM.mat and the resulted T-test image files are
> sometimes different. For example,
>
> By loading 'spmT_0003.img' alone (using spm_vol and spm_read_vols),
> the matrix is (e.g.)
> -3 0 0 81
> 0 3 0 -114
> 0 0 3 -54
> 0 0 0 1
>
> By loading spm.mat:
> SPM.xY.VY(1).mat =
> 3 0 0 -81
> 0 3 0 -114
> 0 0 3 -54
> 0 0 0 1
>
> We can see that the first row is flipped.
>
> This difference actually accounts for the left/right flip of xjview
> (xjview uses the matrix of the t-test image file while SPM uses
> that of SPM.mat). Emily and I have exchanged emails regarding this
> issue but we could not figure this out. Any feedback is appreciated.
>
> Many thanks,
> Xu
>
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask]] On Behalf Of Emily Stern
> Sent: 2006年5月22日 7:49
> To: [log in to unmask]
> Subject: Re: [SPM] Feeding my own T-map (in analyze format) into SPM
>
> Hi Ruth, Ged, and Chris,
> A word of caution when using xjview. There have been some recent
> issues
> where it became apparent that it may be flipping hemispheres.
> Otherwise,
> it's a great program.
> Emily
>
>>>> Christopher Summerfield <[log in to unmask]>
> 05/22/06 5:39 AM >>>
> hi Ruth & Ged,
>
> once you know the FDR-corrected t-value, then it's easy to threshold
> your
> image at that level using xjview
>
> http://people.hnl.bcm.tmc.edu/cuixu/xjView/
>
> all the best,
> Chris
>
>
>
> Christopher Summerfield
> [log in to unmask]
>
> On Mon, 22 May 2006, Ged Ridgway wrote:
>
>> Hi Ruth,
>>
>> I'm also interested in doing this. So far I've worked out that we
>> could use something like:
>>
>> t_crit = spm_uc_FDR(0.001,df,'T',1,tmap_vol)
>>
>> to find the t-threshold corresponding to FDR correction at the 0.001
>> level, where df is the number of degrees of freedom for the t-map,
>> and
>> e.g. tmap_vol = spm_vol('your_tmap.img'). I think this is right for
>> both spm5 and spm2. (see e.g. help spm_uc)
>>
>> Thresholding the t-map is then simple, but I've not yet investigated
>> how to get the thresholded map into the results window. I think it
>> may
>> be necessary to create a basic spm.mat with an appropriate
>> structure, but I'm not sure what the minimal set of fields would be.
>>
>> You'll probably get a more complete answer from someone like John; if
>> not, I'll try to have a look and get back to you if I work it out...
>>
>> Best,
>> Ged.
>>
>>
>> Ruth Heller wrote:
>>> Hi,
>>> I've got my own T-map (in analyze format) that I would like to feed
> into SPM in
>>> order to correct for multiple comparisons and display the results
> using its
>>> graphics window. Is there a way to feed my map into SPM (instead of
> feeding the
>>> original data and performing the whole analysis in SPM)?
>>> Thanks,
>>> Ruth
>>>
>>>
>>>
>>> ----------------------------------------------------------------
>>> This message was sent using IMP, the Internet Messaging Program.
>>>
>>
>
>
>
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