[Brains-users] Getting started - image orientation

[Johnson, Hans J]

Helen,

This is a common problem with ANALYZE file format.  Your data is not compliant with any standard (neither DICOM nor the Analyze 7.5 file format as defined by the developers of the Analyze^{TM} Program).

Even the Analyze^{TM}  main developers have moved away from using Analye 7.5 format over a decade ago because of its serious limitations, and because the community has been very bad about defining many different interpretations of those 348 bytes header file to have vastly different meanings.

I've come to the conclusion that what people call "Analyze" image data very seldom conforms to the original intent or definition of what that file is supposed to contain.

In fact, the entire NIFTI file format initiative was centered around the massive difficulties that arise from different groups attempting to use data in a file formats (yes formats with an 's') that they called Analyze, but were completely in compatible.

I work very closely with the Analyze^{TM} development team to ensure that ITK, and by extension brains2, respected the definition of Analyze7.5 file format as it was originally defined and intended to be used.  If you data does not load properly, that means that it is very likely not compliant with the Analyze7.5 standard.

Hans

--
Hans J. Johnson, Ph.D.
hans-johnson at uiowa.edu<mailto:hans-johnson at uiowa.edu>
Assistant Professor of Psychiatry
University of Iowa Carver College of Medicine
W278 GH, 200 Hawkins Drive
Iowa City, Iowa 52242
Phone:  319-353-8587

From: "Crawford, Helen" <helen.crawford at ucl.ac.uk<mailto:helen.crawford at ucl.ac.uk>>
Date: Thu, 23 Feb 2012 10:46:44 +0000
To: "brains-users at www.nitrc.org<mailto:brains-users at www.nitrc.org>" <brains-users at public.nitrc.org<mailto:brains-users at public.nitrc.org>>
Subject: [Brains-users] Getting started - image orientation

Hi Brains Users,

My name is Helen Crawford and I work in England at University College London in the Huntington's Disease Research Group. I am new to the BRAINS software and have just installed BRAINS2. I seem to have fallen at the first hurdle, loading my images, and am hoping there is a simple solution. When trying to view T1 scans in NIFTI format the sagittal image appears in the axial window, the axial image in coronal and coronal in sagittal. When trying a different format, ANALYZE (.hdr) files, the images appear in the correct windows but are upside down in orientation.

Any help would be greatly appreciated.

Kind regards,

Helen



Helen Crawford
Research Assistant
HD Research Group,
UCL Institue of Neurology,
2nd Floor, Ormond House,
27 Boswell Street,
London,
WC1N 3JZ

Tel: 020 7242 0038
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