The -2/+2 defines the left/right direction of the image in the typical orientation.

The size of the image (number of voxels) is determined by the voxel size and the Bounding Box. I believe that if you set the Bounding Box to [NaN NaN NaN; NaN NaN NaN], then you should get an image with the same dimensions.

Keep in mind, you don't need to write out an image with the same dimensions.



Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Mon, Jul 13, 2015 at 10:41 AM, Lisa McDermott <[log in to unmask]> wrote:
Thank you, Yan Chao-Gan for the DPABI reference. I will take a look at it. 

And thank you Donald, for the response. However, I am still unclear on the dimensions. 

Here's my confusion so far. I checked out the 305T1 using display, and it had a voxel size of [-2 2 2] (not sure about the -2 instead of +2, but that is what it says). So I set the Write part of Normalize: Estimate & Write voxel sizes to [-2 2 2], and I still don't get same dimensions for the wr (normalize: EW) image. In fact, when I calculate the difference between using different voxel sizes ([-2 2 2] instead of [2 2 2]) using imcalc, I get an output that has the vague outlines of the brain (slight difference). I can't attach this because the file is too big. 

Obviously there is some concept I am missing. I don't know how to reconcile between the dimensions of the 305T1 and the generated Normalized image. Or the other related question is, what parameters do I use to generate a normalized image of the same dimensions and voxel size of the 305T1 image? This is in SPM12. 

I am really sorry if this is a silly question. I appreciate any clarification you or anyone else can give regarding this. Thank you. 

Best,

- Lisa

On Sun, Jul 12, 2015 at 10:29 PM, MCLAREN, Donald <[log in to unmask]> wrote:
Lisa,

There are two parts to normalization:
(1) Estimating the normalization parameters; and
(2) Writing normalized images.

The two steps are independent of each other. The write step can write out the images at any resolution that you choose.

You can overlay/display side-by-side the images with any software that doesn't require the same image size: (1) SPM CheckReg; and (2) FIVE come to the top of my mind, but I am sure there are others as well.

When normalization fails - it will really fail. Thus, if the anterior/posterior/inferior/superior/left/right extent of the brain lines up with the template after normalization AND you have all of the brain in the image, then normalization worked.

-Donald


On Sat, Jul 11, 2015 at 2:20 PM, Lisa McDermott <[log in to unmask]> wrote:
Hello all,

Perhaps I am completely misunderstanding this, but when I perform normalization on a dataset, it generates images with dimensions that do not match the 305T1 template or the TPM. I am using SPM12, but I've noticed the same issue with SPM8. What is going on? I noticed this because I've not been able to load both the 305T1 or the TPM on the normalization results using fslview. Does this have something to do with voxel size? If so, how can I get it so that I am able to overlay those datasets on the 305T1 and the TPM images using fslview? 

This brings me to the next question. What is the procedure to see if the normalization step has worked correctly? How do I verify it, or in other words, perform quality control on the normalization results? I understand that the normalization is the one step that would break the most, and I just want to ensure that I'm doing this correctly. I would greatly appreciate any response. Thank you. 

Best,

- Lisa