Hi,
i run "run_first_all -i structural_brain.nii.gz -o
out_structural_brain.nii.gz" -i and i found the followings logs:
Cannot open volume out_structural_brain-L_Accu_corr for reading!
Cannot open volume out_structural_brain-L_Accu_first for reading!
Image Exception : #22 :: ERROR: Could not open image
out_structural_brain_all_fast_origsegs
Aborted
create shapeModel
done creating shapeModel
Error: cannot find image out_structural_brain-R_Thal_first
create shapeModel
done creating shapeModel
Error: cannot find image out_structural_brain-L_Pall_first
create shapeModel
done creating shapeModel
create shapeModel
done creating shapeModel
Error: cannot find image out_structural_brain-L_Hipp_first
Best,
Merlin
[log in to unmask] escribió:
> 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
>>>> >
>>>> > ----------------------------------------------------------------
>>>> > This message was sent using IMP, the Internet Messaging Program.
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > Este mensaje le ha llegado mediante el servicio de correo
>>>> > 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
>>>> >
>>>> > Infomed: http://www.sld.cu/
>>>> > ########################################################################
>>>> > To unsubscribe from the FSL list, click the following link:
>>>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>> >
>>>>
>>>>
>>>> ########################################################################
>>>> To unsubscribe from the FSL list, click the following link:
>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>>
>>>
>>>
>>>
>>> ----------------------------------------------------------------
>>> This message was sent using IMP, the Internet Messaging Program.
>>>
>>>
>>>
>>> --
>>> Este mensaje le ha llegado mediante el servicio de correo
>>> 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
>>>
>>> Infomed: http://www.sld.cu/
>>> ########################################################################
>>> To unsubscribe from the FSL list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>
>>
>>
>> ########################################################################
>>
>> To unsubscribe from the FSL list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>
>
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
>
> --
> Este mensaje le ha llegado mediante el servicio de correo
> 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
>
> Infomed: http://www.sld.cu/
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
--
Este mensaje le ha llegado mediante el servicio de correo 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
Infomed: http://www.sld.cu/
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|