Hi Mark,
the problem with converting PAR/REC 4.2 to analyze format is that analyze format (guess thats what your choosing as output) does not support angulations of images. So the r2agui package just has to assume an orientation, which might not be what you want.
When you convert the PAR/REC images to nifti all should be OK, as r2agui computes the voxel to world matrix in the nii header directly from the PAR file.
It could be that dcm2nii does produce additional mat-files along with the analyze images, similar to what SPM2 did. We chose not to for r2agui, otherwise output would not be 'pure' analyze.
So my advise would be to use nifti output instead of analyze, and use SPM5 or newer. That way you will completely incorporate image orientation and angulation, at least that works very well for us.
Good luck,
Bas
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
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: http://www.neuralnavigator.com
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-----Original Message-----
From: SPM (Statistical Parametric Mapping) on behalf of Mark Gay
Sent: Tue 11/9/2010 21:01
To: [log in to unmask]
Subject: [SPM] coreg images flipped
I have searched the archives without success.
I am using spm8 and I converted Phillips version 4.2 par/rec files into hdr/img files using r2agui. Images were acquired head first supine, anterior-posterior. My problem occurs at the Coreg: Estimate stage.
The Graphics window shows functional SAG image switched left to right and functional transverse image switched anterior to posterior. It further shows anatomical SAG in the top left position on the window switched left to right.
The anatomical SAG image that is in the bottom frame is switched upside down and the anatomical transverse image is sideways also.
r2agui imports the correct parameters from the par file but doesn't convert the images with proper alignment, which is apparent when I view the images after conversion. Do I need to input different r2agui arguments and change the r2agui default.m file?
If so how should it be changed. Any help will be thoroughly appreciated.
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