if i run fslhd i get:
Byte swapping
filename structural_brain.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 256
dim2 256
dim3 128
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.000000
pixdim1 1.000000
pixdim2 1.000000
pixdim3 2.000000
pixdim4 1.000000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 1.000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Unknown
qform_code 0
qto_xyz:1 1.000000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 1.000000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 2.000000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip FSL3.3
aux_file
paul mccarthy <[log in to unmask]> escribió:
> Hi Merlin,
>
> That looks correct, so something else must be failing. What is the
> result of running fslhd on your input image?
> Paul
> On Oct 14 2019, at 10:38 am, [log in to unmask] wrote:
>> the contents of your
>> the contet of $FSLDIR/data/standard/ directory is:
>>
>> avg152T1_brain.nii.gz
>> avg152T1.nii.gz
>> FMRIB58_FA_1mm.nii.gz
>> FMRIB58_FA-skeleton_1mm.nii.gz
>> LowerCingulum_1mm.nii.gz
>> MNI152lin_T1_1mm_brain.nii.gz
>> MNI152lin_T1_1mm.nii.gz
>> MNI152lin_T1_1mm_subbr_mask.nii.gz
>> MNI152lin_T1_2mm_brain_mask.nii.gz
>> MNI152lin_T1_2mm_brain.nii.gz
>> MNI152lin_T1_2mm.nii.gz
>> MNI152_T1_0.5mm.nii.gz
>> MNI152_T1_1mm_brain_mask_dil.nii.gz
>> MNI152_T1_1mm_brain_mask.nii.gz
>> MNI152_T1_1mm_brain.nii.gz
>> MNI152_T1_1mm_first_brain_mask.nii.gz
>> MNI152_T1_1mm_Hipp_mask_dil8.nii.gz
>> MNI152_T1_1mm.nii.gz
>> MNI152_T1_2mm_b0.nii.gz
>> MNI152_T1_2mm_brain_mask_deweight_eyes.nii.gz
>> MNI152_T1_2mm_brain_mask_dil1.nii.gz
>> MNI152_T1_2mm_brain_mask_dil.nii.gz
>> MNI152_T1_2mm_brain_mask.nii.gz
>> MNI152_T1_2mm_brain.nii.gz
>> MNI152_T1_2mm_edges.nii.gz
>> MNI152_T1_2mm_eye_mask.nii.gz
>> MNI152_T1_2mm_LR-masked.nii.gz
>> MNI152_T1_2mm.nii.gz
>> MNI152_T1_2mm_skull.nii.gz
>> MNI152_T1_2mm_strucseg.nii.gz
>> MNI152_T1_2mm_strucseg_periph.nii.gz
>> MNI152_T1_2mm_VentricleMask.nii.gz
>> tissuepriors
>>
>> best,
>> paul mccarthy <[log in to unmask]> escribió:
>> > 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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>> > >
>> > >
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>>
>>
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>>
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>> electronico que ofrece Infomed para respaldar el cumplimiento de
>> las misiones del Sistema Nacional de Salud. La persona que envia
>> este correo asume el compromiso de usar el servicio a tales fines y
>> cumplir con las regulaciones establecidas
>>
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