NIFTI

Questions about BrainVisa usage and installation

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ekke
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Joined: Mon May 29, 2006 10:47 am

NIFTI

Postby ekke » Wed Jun 14, 2006 6:41 pm

Dear BrainVISA developers

are there plans to support the NIFTI-1 format ?
Or are there workarounds for using data sets generated by SPM5?

All the best
Ekkehard
Ekkehard Kuestermann, PhD
Universitaet Bremen
c/o FB2, AG Leibfritz
Postfach 33 04 40
D-28334 Bremen
Tel: +49 (0)421 - 218 -2919
Email: ek@tomo.uni-bremen.de

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Jean-Francois Mangin
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Postby Jean-Francois Mangin » Mon Jun 19, 2006 9:20 am

There are plans but no deadline :)
But I hope SPM5 or the NIH is providing some conversion tools...

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Yann Cointepas
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Postby Yann Cointepas » Mon Jun 19, 2006 1:56 pm

As Jean-François said, the current version does not recognize this format. However, if you have a converter program between NIFTI and one of the formats reconized by BrainVISA, it is possible to write a converter process that will be called automatically whenever a NIFTI image is used with a non NIFTY aware process.

PeterK
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Joined: Fri Mar 05, 2004 3:18 pm

Postby PeterK » Wed Jun 21, 2006 2:19 pm

FSL has the most stable converter at the moment. It is called avwchfiletype. It will convert from NIFTI to ANALYZE.

joly
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Postby joly » Tue Sep 11, 2007 9:47 am

Hi all,
Since I also need recently my SPM5 results (spmT images) written in NIFTI format to be readable as ANALYZE format in Anatomist. As a converter, I propose to use a combine code of both SPM versions. Read your NIFTI mage with SPM5 and write the volume in a new ANALYZE file with spm99 (or SPM2) routines. For handiness put the code in a toolbox directory.
Olivier

Code: Select all

function V=ToAnalyze(P)
% Convert your Nifti spmT images in Analyze format for compatibility with Anatomist (or others)
% P is your nifti (spmT or other) image (a matrix of filenames)
%
% Olivier Joly - PhD student KUL - Leuven, Belgium - 09/11/2007
if nargin<1
[P,sts] = spm_select([1 Inf],'image','Select your nifti images...');
end
for i=1:size(P,1)
V=spm_vol(P(i,:));
[Y,XYZ]=spm_read_vols(V);
Vout.fname=[V.fname(1:end-4) '_ANLYZE.img']; % you can change the default name...
Vout.mat=V.mat;
Vout.dim=V.dim;
Vout.dim(4)=16;
Vout.pinfo=V.pinfo;
Vout.descrip=V.descrip;
V = spm_write_vol99(Vout,Y); %% spm_create_image99, spm_write_plane99,spm_type99,spm_hwrite99 are the SPM99 functions called by spm_write_vol99.
end

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Yann Cointepas
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Postby Yann Cointepas » Tue Sep 11, 2007 10:37 am

The developpement version of BrainVISA/Anatomist now support NIFTI format. We are trying to make a new stable version as soon as possible but there is still work to do and we cannot give a release date yet.

sdika
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Joined: Fri Dec 21, 2007 10:47 am

Postby sdika » Fri Jan 25, 2008 10:54 am

Dear developpers,

would it be possible that the future release of brainvisa read/write the gzipped nifti or analyze files ?

Michaël

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riviere
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Postby riviere » Sun Jan 27, 2008 5:08 pm

The future release will support NIFTI-1 and gzipped NIFTI-1 for read/write.
Denis


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