Hello FSL experts,
I've been running into a persistent pre-processing problem. My first level analyses seem to be running as expected, but there is an issue with registering examplefunc to the highres image. I've pasted my registration output below. My understanding is that FEAT can't find my examplefunc2highres.mat file, and doesn't like the size of the sla.png files. What I've done up to this point has been pretty routine stuff that hadn't given me problems in the past - dicom to nifti conversion, structural betting (robustfov for some tougher to extract T1s), fsl motion outliers, and automating FEAT for my first level analyses. For what it's worth, I'm running FSL 5.09. Any advice is greatly appreciated!
Best,
Ahmet
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Registration
/bin/mkdir -p /media/sf_ADHD_MRI_Study/ADHD_MRI_FINAL/BRAIN_DATA/ADHD_014/ADHD_014_run_001.feat/reg
/usr/share/fsl/5.0/bin/fslmaths /media/sf_ADHD_MRI_Study/ADHD_MRI_FINAL/BRAIN_DATA/ADHD_014/ADHD_014_struc_brain highres
/usr/share/fsl/5.0/bin/fslmaths /media/sf_ADHD_MRI_Study/ADHD_MRI_FINAL/BRAIN_DATA/ADHD_014/ADHD_014_struc.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
Running FAST segmentation FLIRT pre-alignment Running BBR 0.449398 0.999891 -0.014108 0.004301 0.000000 0.013962 0.999378 0.032395 0.000000 -0.004756 -0.032332 0.999466 0.000000 -0.753815 4.741785 -0.794031 1.000000
/usr/share/fsl/5.0/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat
/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
Images aren't the same size!
Cannot open sla.png for reading
Segmentation fault
Images aren't the same size!
Cannot open sla.png for reading
Segmentation fault
Cannot open example_func2highres1.png for reading
Segmentation fault
/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
/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
/usr/share/fsl/5.0/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear
Found file: example_func2standard.mat.
/usr/share/fsl/5.0/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat
/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
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