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Re: [SCIRUN-USERS] left/right for MR volumes

Chronological Thread 
  • From: Darren Weber <>
  • To: Chris Butson <>
  • Cc:
  • Subject: Re: [SCIRUN-USERS] left/right for MR volumes
  • Date: Sat, 25 Feb 2006 00:27:46 -0800
  • Organization: UCSF Department of Radiology

Hi Chris,

I have some code and notes about Analyze, see

I don't know anything about Teem i/o functions.

Best, Darren

Chris Butson wrote:

I have noticed a discrepancy in the way Teem handles left/right for MR volumes. I have a 160 slice T1 MR acquired from a Siemens scanner. This particular patient has a very asymmetric brain so left/right are easy to identify from inspection. If I load the patient data into SCIRun either from raw dicom files (using DicomNrrdReader) or from a hdr/img volume (generated using Analyze, loaded into scirun with AnalyzeNrrdReader) then the 3D brain volume is flipped left/right. If I view the same hdr/img volume or dicom series in Analyze then left/right are rendered correctly in 3D.

The radiologists convention dictates that for patients who are head first and supine in the magnet, you should envision looking through the feet so the right side of the brain is on the left side of the screen for axial slices. However, 3D renderings are unambiguous in terms of left/right so no convention is needed. So it is a little odd that the scirun renderings seem to be flipped. More disturbing is the difference in 3D rendering from the same data with different pieces of software. Has anyone else noticed this problem? Is there an explanation for this behavior that I am missing?


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Darren L. Weber, Ph.D.
Visiting Postdoctoral Scholar

Dynamic Neuroimaging Laboratory, Department of Radiology,
University of California, San Francisco,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.

Tel: +1 415 353-9444
Fax: +1 415 353-9421

"To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself."
--Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

== The SCIRun Users mailing list: send email to   ==
== for more details.                                                     ==
== Please acknowledge use of SCIRun in your papers and reports:          ==
==   see         ==

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