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 Hammers, MD PhD

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

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?

-----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:
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....).