Dear Maki,
The output you are getting is not Analyze, it is a NIFTI pair.
If you want a single NIFTI file (.nii) then you should set the
environment variable FSLOUTPUTTYPE to be NIFTI
(or NIFTI_GZ if you also want it compressed to .nii.gz).
You should have a line setting this variable in one of
your shell setup files (.bash_profile, .profile or .bashrc).
I don't know why it is set to NIFTI_PAIR at the moment,
as that is unusual, with NIFTI_GZ being the default.
All the best,
Mark
On 25 Jul 2011, at 08:44, Maki Kasahara wrote:
> Dear Matt,
>
> Thank you very much for your reply.
>
> The output of
> env | grep FSL
>
> is as follows:
>
> FSLMULTIFILEQUIT=TRUE
> FSLTCLSH=/usr/bin/tclsh
> FSLMACHINELIST=
> FSLREMOTECALL=
> FSLWISH=/usr/bin/wish
> FSLBROWSER/etc/alternatives/x-www-browser
> FSLDIR=/usr/share/fsl
> FSLLOCKDIR=
> FSLOUTPUTTYPE=NIFTI_PAIR
>
> With many thanks,
>
> Maki Kasahara
> !
>
>
> Date: Fri, 22 Jul 2011 12:22:14 -0500
> From: [log in to unmask]
> Subject: Re: [FSL] Eddy current correction output
> To: [log in to unmask]
>
> That sounds like your FSL environment is not set up properly. What is the output of:
>
> env | grep FSL
>
> Peace,
>
> Matt.
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Maki Kasahara
> Sent: Friday, July 22, 2011 11:47 AM
> To: [log in to unmask]
> Subject: [FSL] Eddy current correction output
>
>
> Dear FSL list,
>
> I have a problem that when I feed *.nii.gz image to eddy_correct, I get output images in Analyze format (.img and .hdr).
>
> This seems to cause problems later on when I try to run tbss_2_reg
>
> Therefore, I would be grateful if you could let me know how I may be able to resolve this problem.
>
> With best wishes,
>
> Maki Kasahara
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