Experienced FSLers:
Registration stopped working for me after I reinstalled Ubuntu (16.0.4) and FSL (5). I am wondering if anyone can help me debug. When running first-level processing on a scan, here is the registration output; thank you for any help you can offer!
Registration
/bin/mkdir -p /home/scheffjd/Desktop/4009.feat/reg
/usr/share/fsl/5.0/bin/fslmaths /home/scheffjd/Desktop/4009/T1-brain highres
/usr/share/fsl/5.0/bin/fslmaths /home/scheffjd/Desktop/4009/T1-brain highres_head
/usr/share/fsl/5.0/bin/fslmaths /usr/share/fsl/data/standard/MNI152_T1_1mm_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: 22913 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: 22929 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...
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