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SPM  February 2012

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Subject:

Re: setting origin to ac

From:

"Neggers, S.F.W." <[log in to unmask]>

Reply-To:

Neggers, S.F.W.

Date:

Fri, 17 Feb 2012 16:26:10 +0000

Content-Type:

text/plain

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Sorry John, David, I see you already answered to most issues I just answered. Glad to see we agree ;-)

________________________________
From: Neggers, S.F.W.
Sent: Friday, February 17, 2012 5:23 PM
To: MCLAREN, Donald
Cc: [log in to unmask]
Subject: RE: [SPM] setting origin to ac

Hi Donald,  David,

Donald: I remember how you learned about *.mat files in spm8, that was after a question from me about 4D data ;-)

*.mat files are only used for 4D data in spm8 as far as im aware of. For realigning (not reslicing) oir coregistering or manually displacing 3D time series data I never get *.mat files as used to be the case in spm2 and earlier. It is not needed for 3D data as this info is in the header per image.

David: I guess you can reuse your old data right away. When doing it anew, take care that your images roughly match the MNI template before starting. There is no such thing anymore as an 'origin' in nifti files that is actually used. Things work different for nii data.

That does NOT mean, in general, that you do not have to manually align your images anymore in spm5/8. It is STILL needed (just not with origin setting anymore). As Donald said, your images need to approximately match MNI before doing any further preprocessing.

When you are lucky your old Analyze 7.5 format data is already close to MNI as you aligned them already by using mat files (in spm99), but i cant tell without inspecting them. My other remark about raw format means that, for most institutes/scanners ive seen, conversion from Dicom or other raw scanner format to nifti yields files that are often close enough to MNI to start right away. But dont COUNT on it.

Finally: take proper care about flipping L/R too when using analyze images in SPM8. In Analyze images, this information about image handedness is not stored in the image header, you need to tell SPM. For nifti, this is less of an issue as handedness is encoded in the header.

Actually, SPM8 can, in my experience, handle quite a difference between starting positions of images automatically during coregistration/normalization. Indeed, when orientation is off by 10-20 degrees, and location by several cm, your usually fine and SPM will succeed in matching scans to eachother or the template. With bigger differences this might fail. But ALWAYS check your results to make sure, there are no guarantees.

Good luck,

Bas



________________________________
From: MCLAREN, Donald [[log in to unmask]]
Sent: Friday, February 17, 2012 4:15 PM
To: Neggers, S.F.W.
Cc: [log in to unmask]
Subject: Re: [SPM] setting origin to ac

Bas/David,

For fMRI data, SPM8 still relies on the *.mat files. The reason for this is that the nifti file can only have 1 transformation matrix in it (I learned this about a month ago). If you remove the *.mat files from a directory and display the images, you will notice that they shift. The classic example is motion correction. After you motion correct the data, you have a mat file. If you remove the mat file, you undo the motion correction.

As for reading analyze 7.5 files. This shouldn't be a problem. I've read these files into SPM8 without any problems.

If you try to use old SPM.mat files, you will have some issues as the contents of the header that is read by SPM5/8 has changed.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Office: (773) 406-2464
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On Fri, Feb 17, 2012 at 10:05 AM, S.F.W. Neggers <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi David,

Let's assume you used data in Analyze 7.5 format in spm99. Is that correct?

SPM8 uses the Nifti format, no *mat files are required anymore as the voxel-to-world mapping (that was stored in the mat-file for spm99 and spm2) is now saved in the nifti file header directly. The origin is also implicitely 'stored'  in the voxel to world matrix. There is no explicit origin anymore for Nifti data.

Your task is now much more general: make sure all your images are roughly in correspondance with the template you want to eventually register all your data to (usually an MNI template).

I never tried it, but perhaps spm8 can read Analyze images, and write results out in correct nii? Then you'd be done.

When that doesnt work: the information about the correct displacements is already in your Aanalyze + mat files, so you might be able to write a conversion script that converts your Analyze files to nifti taking into account the *mat files (and saving the appropriate voxel-2-world matrix in the nii headers). That would save you the hassle. Perhaps such a script is already out there?

On another note: most raw formats (Dicom, PAR/REC) can be converted to nifti nowadays, creating images already that are in quite good correspondance with MNI, and there is no need anymore for manual realignment. At least that is how it is for us. This will strongly depend on your pipeline from the scanner to your computer. And of course you would need the old raw scanner data.

Good luck,

Bas






Op 17-02-12 15:28, David Andel schreef:

Dear SMPers

I have analysed a number of scans years ago in SPM99.
For this purpose I have set the origin to the anterior commissure manually for each scan.

Now I want to reanalyse the whole study in SMP8 again.
Is there a way to apply the origins set in SPM99 for each scan now in SPM8 so that I don't have to manually redo all this?
That would save me quite some time.
I guess this must be stored in some of the *.mat files, doesn't it?

Thank you and best regards,
David



--
--------------------------------------------------
Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center

Visiting : Heidelberglaan 100, 3584 CX Utrecht
          Room B.01.1.03
Mail     : Huispost B01.206, P.O. Box 85500
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Fax      : +31 (0)88 7555443<tel:%2B31%20%280%2988%207555443>
E-mail   : [log in to unmask]<mailto:[log in to unmask]>
Web      : http://www.neuromri.nl/people/bas-neggers
        : http://www.neuralnavigator.com (CEO)
--------------------------------------------------


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