Hello Chuck.
These messages are simply informative - telling you that no existing registration exists and so one will be generated!
Kind Regards
Matthew
> I have a researcher who is getting the following output for the registration step:
>
> "I have issue with the group mean contrast images I get in the end. I
> do not have the skull removed and they are fuzzy, meaning that normalization
> and registration might not go smoothly. As I told you in
> the log for January I saw that the images files are missing. Below you
> can see the logs themselves."
>
> In analyses done in November, the "did not find" messages did not occur. Since then,
> I had updated to FSL 5.0.2 and now we get these messages regarding missing .mat
> files. Are the messages simply informative, or indicative of some problem?
>
> Thanks,
> Chuck
>
>
> /bin/mkdir -p /vxfsvol/home/research/pslab/analysis/003_cg1.feat/reg
>
>
> /usr/share/fsl/5.0/bin/fslmaths /vxfsvol/home/research/pslab/test/0002801/163_013_MPRAGE_20130108/0002801_20130108_163_013_MPRAGE highres
>
>
> /usr/share/fsl/5.0/bin/fslmaths /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain standard
>
> did not find file: example_func2highres.mat. Generating transform.
>
> /usr/share/fsl/5.0/bin/flirt -in example_func -ref highres -out example_func2highres -omat example_func2highres.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
>
>
> /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
>
>
> /bin/rm example_func2highres1.png
>
> 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
>
> --
> Chuck Theobald
> System Administrator
> The Robert and Beverly Lewis Center for Neuroimaging
> University of Oregon
> P: 541-346-0343
> F: 541-346-0345
>
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