Dear Maki,
If this is a central installation but you do not like the settings
then you can change them for your account only by putting in
the line:
FSLOUTPUTTYPE=NIFTI_GZ
export FSLOUTPUTTYPE
into your .bashrc file (or .bash_profile or .profile file - whatever
one you currently have already) and this will override the
central choice just for your account.
All the best,
Mark
On 25 Jul 2011, at 09:25, Maki Kasahara wrote:
> Dear Mark,
>
> Thank you very much for your explanation!
> I am using FSL that is installed in our institute's computing system, so I will make an enquiry to the computing officer.
>
> With many thanks and best wishes,
>
> Maki
>
> > Date: Mon, 25 Jul 2011 08:59:03 +0100
> > From: [log in to unmask]
> > Subject: Re: [FSL] Eddy current correction output
> > To: [log in to unmask]
> >
> > 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]
> &g! t; >
> > > 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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