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Hi Merlin,

We don't currently recommend or support installations from synaptic - instead, I would encourage you to install FSL by following the instructions here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
As for the first_flirt error, I am guessing that some files are missing from your FSL installation. What is the contents of your $FSLDIR/data/standard/ directory?
Paul
On Oct 13 2019, at 10:00 pm, [log in to unmask] wrote:
> Hi,
> I installed FSL using synaptic, I installed the fsl-5.0-core packages,
> this created a directory with the fsl utilities in / usr / bin /, in
> this directory I can find the fsl programs as follows:
>
> /usr/bin/fsl5.0-Asl
> /usr/bin/fsl5.0-Bet
> /usr/bin/fsl5.0-ConcatXFM
> /usr/bin/fsl5.0-Fast
> /usr/bin/fsl5.0-Fdt
> /usr/bin/fsl5.0-Feat
> .
> .
> .
> etc
>
>
> But I also have another directory: /usr/share/fsl/5.0
> In this directory there is a shortcut to a bin folder that has the
> following programs:
>
>
> file: ///usr/share/fsl/5.0/bin/bet
> file: ///usr/share/fsl/5.0/bin/Bet
> file: ///usr/share/fsl/5.0/bin/checkFEAT
> file: ///usr/share/fsl/5.0/bin/cluster2html
> file: ///usr/share/fsl/5.0/bin/concat_bvars
> file: ///usr/share/fsl/5.0/bin/ConcatXFM
> file: ///usr/share/fsl/5.0/bin/design_ttest2
> file: ///usr/share/fsl/5.0/bin/dual_regression
> file: ///usr/share/fsl/5.0/bin/easythresh
> file: ///usr/share/fsl/5.0/bin/eddy_correct
> file: ///usr/share/fsl/5.0/bin/epi_reg
> file: ///usr/share/fsl/5.0/bin/estnoise
> file: ///usr/share/fsl/5.0/bin/extractfidparams
> file: ///usr/share/fsl/5.0/bin/extracttxt
> file: ///usr/share/fsl/5.0/bin/fabber_var
> file: ///usr/share/fsl/5.0/bin/Fast
> .
> .
> .
> etc
>
> in this directory the programs do not start with "fsl5.0"
> In the .bashrc you will find:
> FSLDIR = / usr / share / fsl / 5.0
> . $ {FSLDIR} /etc/fslconf/fsl.sh
> PATH = $ {FSLDIR} / bin: $ {PATH}
> export FSLDIR PATH
>
> When I try to run is the following program:
> first_flirt structural structural_to_std_sub
> I get:
> initial registration 0
> Stage 2: use subcortical mask
> terminate called after throwing an instance of 'NEWMAT :: SingularException'
> Aborted
>
> Something similar happens with the following FSL programs, and I can't
> do anything with FSL.
> I use Debian 10.
>
> I would appreciate any help.
> Many thanks in advance,
> Best,
> Merlin
>
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