Hi,
Can you look at the file:
*_fast_wmseg.nii.gz
and see if that contains a useful white matter segmentation?
I cannot be sure, but sometimes I've seen problems like this because the segmentation of the anatomical image has failed.
All the best,
Mark
> On 7 Nov 2017, at 22:18, Ellie Morgenroth <[log in to unmask]> wrote:
>
> Dear all,
> I set up a first level FEAT analysis and get the following registration log. I found that others had similar problems before but no solution. The analysis runs anyway, however the registration of functional data does not seem to happen.
> The functional data is 420 volumes from a multi-band sequence and I'm running fsl on an ubuntu 16.04 vm.
>
> Any help would be greatly appreciated, let me know if you need any more details.
> Thank you!
> Ellie
>
> ""
> /bin/mkdir -p /home/xx/xx_run1.feat/reg
>
>
> /usr/share/fsl/5.0/bin/fslmaths /home/xx/20170913_111708t1mprsagisos002a1001_brain highres
>
>
> /usr/share/fsl/5.0/bin/fslmaths /home/xx/20170913_111708t1mprsagisos002a1001.nii.gz highres_head
>
>
> /usr/share/fsl/5.0/bin/fslmaths /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain standard
>
> 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: 102863 Aborted (core dumped) $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: 102871 Segmentation fault (core dumped) $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 (core dumped)
>
> Cannot open example_func2highres1.png for reading
> Segmentation fault (core dumped)
> 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 -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
>
>
> /usr/share/fsl/5.0/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
> terminate called after throwing an instance of 'NEWMAT::SingularException'
> Aborted (core dumped)
>
>
> /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
>
>
> /bin/rm highres2standard1.png
>
>
> /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 (core dumped)
>
> Cannot open example_func2standard1.png for reading
> Segmentation fault (core dumped)
> Error in slicer input, exiting...
> ""
