Then perhaps avoid PVELAB (dont know the format)? From most scanners (Philips and Siemens, for example), it is possible to get to nifti data more or less directly. At Philips the scanner can nowadays create nifti for you directly, or through DICOM. At Siemens I think one uses mosaic or dicom, then nifti, but I am not very experienced with Siemens.
Anyway, good luck,
Bas
--------------------------------------------------
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
3508 GA Utrecht, the Netherlands
Tel : +31 (0)88 7559609
Fax : +31 (0)88 7555443
E-mail : [log in to unmask]
Web : http://www.neuromri.nl/people/bas-neggers
: http://www.brainsciencetools.com (CEO)
--------------------------------------------------
________________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Pieter Vandemaele [[log in to unmask]]
Sent: Wednesday, January 30, 2013 3:08 PM
To: [log in to unmask]
Subject: Re: [SPM] image orientation mismatch
The problem is that PVELAB does not support nifti, even in the newer 2012 version. I had a discussion with the lab who programmed it, but they still use Analyze and have no plans to support Nifti.
If possible, I always avoid image conversions, but in this case it is inevitable.
Thanks for the feedback.
Pieter
Op 30/01/2013 15:05, MCLAREN, Donald schreef:
It means that one of your images is shifted. If you applied the same
transforms to all images, then you should end up with the same image
dimension and location. Since the same process results in 2 different
values, it means that you changed the images in PVELAB somehow OR you
didn't apply the same transforms to all images.
I would look more closely at PVELAB to see why its shifting some of
the images. As Bas said, try to avoid using ANALYZE format images as
they don't contain the necessary information.
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 Wed, Jan 30, 2013 at 8:39 AM, Pieter Vandemaele
<[log in to unmask]><mailto:[log in to unmask]> wrote:
Dear all,
I want to do an anova analysis with 2 factors, age(young/old) and corrected
(yes/no).
In fact, all images are processed until normalisation. Then all images are
converted to Analyze and processed in another program (PVELAB) and converted
back to Nifti and smoothed.
The original images are also converted back Nifti and smoothed so all images
underwent the same transformation.
The corrected and uncorrected images are then used in the Anova.
I got the following error running the Anova module in spm_check_orientations
Running 'Factorial design specification'
Mapping files :
** The images do not all have same orientation and/or voxel sizes. **
The function assumes that a voxel in one image corresponds exactly
with the same voxel in another. This is not a safe assumption if
the orientation information in the headers or .mat files says that
the images are oriented differently. Please ensure that you process
all data correctly. For example, you may have realigned the images,
but not actually resliced them to be in voxel-wise alignment.
Here are the orientation matrices of the image volumes. This list
can be used to determine which file(s) are causing the problem.
[-2 0 0 80; 0 2 0 -114; 0 0 2 -52] file 1
[-2 0 0 80; 0 2 0 -114; 0 0 2 -53] file 2
I now show only the difference between corrected and uncorrected in the
factorial design.
Is this due to rounding errors like mentioned in
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0708&L=SPM&P=R35432&I=-3&d=No+Match%3BMatch%3BMatches
How can I correct for this, what is the meaning of -52 and -53?
Are
Regards
Pieter
--
[cid:part1.01020006.01060404@UGent.be]
Pieter Vandemaele, MSc-Ing
GIfMI Site Manager
Ghent Institute for Functional and Metabolic Imaging
MR Department -1K12
Ghent University Hospital
De Pintelaan 185
9000 Ghent - BELGIUM
[log in to unmask]<mailto:[log in to unmask]> tel: +32 (0)9 332 48 20
http://gifmi.ugent.be fax: +32 (0)9 332 49 69
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