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Dear Ed,


If you have the *_seg_sn.mat file, you possibly have the bias- 
corrected structural image already - it's called m* with *=name of  
your original structural image used as input to SEGMENT and should be  
in the same directory as the *seg_sn.mat.

If its creation was disabled during SEGMENT, you'd have to change the  
options - I don't have matlab/SPM where I am right now, but I believe  
it's within the list of options which files you want created and in  
which space.

Nearly there!

All the best,

Alexander

---------------------------------
Alexander Hammers, MD PhD



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On 28 May 2010, at 23:16, Modestino, Edward J *HS wrote:

> Hello,
> I am still having issues with this.  I have gotten to the  
> normalization procedure.  I noticed that there is a mention in the  
> manual on page 231 on an example data set that "If you wish to  
> superimpose a subject's functional activations on their own anatomy,  
> you will need to apply the spatial normalization parameters to their  
> (bias-corrected) anatomical image."
>
> Following this example data set instructions, I cannot find the step  
> in the processing where this bias-corrected structural image was  
> created to use in the normalization with the *_seg_sn.mat for  
> normalization.  Can someone please let me know how and in what  
> process this is created?
> Thanks,
> Ed
>
> -----Original Message-----
> From: Jonathan Peelle [mailto:[log in to unmask]]
> Sent: Friday, May 28, 2010 11:08 AM
> To: Modestino, Edward J *HS
> Cc: [log in to unmask]
> Subject: Re: [SPM] Coregistration/activity outside occipital lobe
>
>> The order in processing I am using is:
>> (1) Realignment
>> (2) Slice time correction
>> (3) Coregistration...
>>
>> If I follow what I said below:
>> Coregister:
>> ref.img: T1 structural image
>> sou.img: Mean fMRI
>> other images: all the realigned fMRI volumes
>>
>> Do I choose in coregistration under "other images" the realigned  
>> images and NOT the slice time corrected images?
>
> You want to choose whatever images you'll be doing the stats on, so in
> this case, the slice-time corrected images.  (It wouldn't hurt to
> select the realigned images, in addition....).
>
> Jonathan