Hi Antonios-Constantine,
these two warning messages only refer to one step in the creation of the first-pass and second-pass templates (they're symmetrical so need all the GM to be flipped along the x-axis). It's fine...
Cheers,
Gwen
--- En date de : Jeu 9.10.08, Antonios-Constantine Thanellas <[log in to unmask]> a écrit :
> De: Antonios-Constantine Thanellas <[log in to unmask]>
> Objet: Re: [FSL] Problems finding fnirt --config files solved.
> À: [log in to unmask]
> Date: Jeudi 9 Octobre 2008, 19h14
> Hi Jesper,
> after this change i didn't receive any error log file
> and the analysis finished normally.
> There were only 2 warning log files the fslvbm2e.o26898 and
> fslvbm2c.o2223 about flipping left/right orientation as
> det<0
> Is it something that i should take into consideration or
> just ignore it?
> Thank you
> Antonios-Constantine Thanellas
>
>
>
>
> ----- Original Message ----
> From: Jesper Andersson <[log in to unmask]>
> To: [log in to unmask]
> Sent: Tuesday, October 7, 2008 1:07:06 PM
> Subject: Re: [FSL] Problems finding fnirt --config files
> solved.
>
> Hi Antonios,
>
> I looked a little more closely at your problem in the
> september archive.
>
> It seems to me that in your case fnirt actually finds the
> configuration
> file, but then fails to find the --refmask. This is caused
> by a path to
> the refmask being hardcoded in that version of the
> GM_2_MNI152GM_2mm.cnf
> file.
>
> You should edit the GM_2_MNI152GM_2mm.cnf file so that the
> --refmask line
> reads
>
> --refmask=MNI152_T1_2mm_brain_mask_dil
>
> instead of
>
> --refmask=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz
>
> as it does now. This has also been fixed for the next
> release.
>
> Good Luck Jesper
>
>
> > Hi Jesper,
> >
> > My path doesn't contain any dot (.) ,though the
> problem still exists. To
> > be
> > more specific my path is specified as follows:
> > $FSLDIR/etc/flirtsch ,where echo $FSLDIR =
> usr/share/fsl.
> >
> > Regarding the problem i've encountered,details
> were mentioned in
> > September's
> > archives with title "following different order
> on VBM analysis steps"
> >
> > Any ideas?
> > Thank you
> > Antonios-Constantine Thanellas
> >
> >
> >
> > On Mon, 6 Oct 2008 13:00:02 +0200, Jesper Andersson
> > <[log in to unmask]>
> > wrote:
> >
> >>Dear everyone,
> >>
> >>there has been several mails about fnirt not
> finding the
> >>configuration files it is supposed to find. This
> has now been fixed
> >>and will be part of the next release.
> >>
> >>It turns out that the problem occurs when there is
> a "dot" (.)
> >>somewhere in the path ${FSLDIR}/etc/flirtsch/. For
> example if FSLDIR
> >>is set to /usr/local/fsl4.1
> >>
> >>Meanwhile you can work around it by copying the
> existing .cnf files
> >>in ${FSLDIR}/etc/flirtsch/ so that there are
> versions both with and
> >>without the extension. Just remember to delete the
> extension free
> >>ones when you install the next release of fsl.
> >>
> >>Good Luck Jesper
> >
> >
> >
> >
>
>
>
>
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