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Re: [Seg3D] Seg3D2 export segmentations

Chronological Thread 
  • From: Pieter Vandemaele <>
  • To: Timothy Brown <>,
  • Subject: Re: [Seg3D] Seg3D2 export segmentations
  • Date: Tue, 7 Mar 2017 15:30:43 +0100
  • Organization: Universiteit Gent

Analyze is deprecated and support should be removed from all current versions of neuroimaging software packages.
Most modern packages do only support Analyze for backwards compatibility but do recommend the use of NIfTI.

A google search yields this:,+nifti+to+nrrd,+and+nrrd+to+nifti

You should consider converting your processing pipeline to NIfTI unless you have a very good reason.

You can convert NRRD to NIfTI with Mevislab. The schematic for that is using ITK:

Then you can use Matlab to convert to Analyze: is also able to do some conversion

Keep in mind that you do 2 conversions, each with his own drawbacks. Always check the data after each conversion step to make sure that Left/Right and origin issues are resolved!

Op 7/03/2017 om 15:03 schreef Timothy Brown:
Hi All,

We have been using Seg3D version 1.2 to create masks in Analyze format.

We have begun using Seg3D2 and I see that default output for segmentations is nrrd

Is there any option to export to Analyze format using newer version of Seg3D2, or can anyone recommend any scripting utilities to convert from nrrd to Analyze?

Thanks for any help you can provide.


Timothy Brown, P.E.           email:
Associate Research Engineer   phone: 410.516.7551
Center for Imaging Science    fax:   410.516.4557
Johns Hopkins University
305 Clark Hall
3400 N. Charles Street
Baltimore, MD 21218

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Re: Netwerk MR afdeling UZGent

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 tel: +32 (0)9 332 48 20 fax: +32 (0)9 332 49 69
ORCID ID 0000-0002-4523-2476

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