Hello,
In your melodic output directory, can you tell me the result of running the two commands:
ls -al reg
more reg/example_func2highres.mat
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 15 Jun 2016, at 15:37, Helena Blumen <[log in to unmask]> wrote:
>
> Hi Everyone,
> I recently installed fsl 5.0 (via neurodebian) on my ubuntu machine. When trying to run standard fsl-MELODIC analyses that I have run before I get the following errors during registration. Anyone else have the same or a similar problem?
>
> Thanks!
>
> Helena
>
> did not find file: example_func2highres.mat. Generating transform.
>
> /usr/share/fsl/5.0/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> /usr/share/fsl/5.0/bin/epi_reg: line 378: 29018 Aborted $FSLDIR/bin/flirt -ref ${vrefhead} -in ${vepi} -dof 6 -cost bbr -wmseg ${vout}_fast_wmseg -init ${vout}_init.mat -omat ${vout}.mat -out ${vout} -schedule ${FSLDIR}/etc/flirtsch/bbr.sch
> Could not open matrix file example_func2highres.mat
> /usr/share/fsl/5.0/bin/epi_reg: line 378: 29077 Segmentation fault $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline
> Running FAST segmentation FLIRT pre-alignment Running BBR
>
> /usr/share/fsl/5.0/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres1.png ; /usr/share/fsl/5.0/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres2.png ; /usr/share/fsl/5.0/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png example_func2highres2.png
> Image Exception : #22 :: ERROR: Could not open image example_func2highres
>
> Cannot open sla.png for reading
> Segmentation fault
>
> Cannot open example_func2highres1.png for reading
> Segmentation fault
> Error in slicer input, exiting...
>
> /bin/rm example_func2highres1.png
> /bin/rm: cannot remove 'example_func2highres1.png': No such file or directory
>
> did not find file: highres2standard.mat. Generating transform.
>
> /usr/share/fsl/5.0/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -interp trilinear
>
>
> /usr/share/fsl/5.0/bin/fnirt --iout=highres2standard_head --in=highres_head --aff=highres2standard.mat --cout=highres2standard_warp --iout=highres2standard --jout=highres2highres_jac --config=T1_2_MNI152_2mm --ref=standard_head --refmask=standard_mask --warpres=3,3,3
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> Aborted
>
>
> /usr/share/fsl/5.0/bin/applywarp -i highres -r standard -o highres2standard -w highres2standard_warp
> Image Exception : #22 :: ERROR: Could not open image highres2standard_warp
> An error occured while reading file: highres2standard_warp
>
>
> /usr/share/fsl/5.0/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> Aborted
>
>
> /usr/share/fsl/5.0/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard1.png ; /usr/share/fsl/5.0/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard2.png ; /usr/share/fsl/5.0/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png highres2standard2.png
> Image Exception : #22 :: ERROR: Could not open image highres2standard
>
> Cannot open sla.png for reading
> Segmentation fault
>
> Cannot open highres2standard1.png for reading
> Segmentation fault
> Error in slicer input, exiting...
>
> /bin/rm highres2standard1.png
> /bin/rm: cannot remove 'highres2standard1.png': No such file or directory
>
>
> /usr/share/fsl/5.0/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat
> Could not open matrix file example_func2highres.mat
> Cannot read input-matrix
>
> did not find file: example_func2standard.mat. Generating transform.
>
> /usr/share/fsl/5.0/bin/flirt -in example_func -ref standard -out example_func2standard -omat example_func2standard.mat -cost corratio -dof -searchrx - -searchry - -searchrz - -interp trilinear
> Unrecognised option -
>
>
> /usr/share/fsl/5.0/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard1.png ; /usr/share/fsl/5.0/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard2.png ; /usr/share/fsl/5.0/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png example_func2standard2.png
> Image Exception : #22 :: ERROR: Could not open image example_func2standard
>
> Cannot open sla.png for reading
> Segmentation fault
>
> Cannot open example_func2standard1.png for reading
> Segmentation fault
> Error in slicer input, exiting...
>
>
>
> Helena M. Blumen, PhD.
> Assistant Professor
> Division of Geriatrics
> Department of Medicine
> Albert Einstein College of Medicine
> E-mail: [log in to unmask]
> Office Phones: (718) 430 3810
|