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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