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Hi Erin, What are the files you're inputting into the analysis? It seems like the issue might be in creating the example_func2highres.mat file. Do you have a transformed example_func2highres.nii file? Best, Rachelle On Mon, Apr 9, 2018 at 7:10 PM, Erin Walsh <[log in to unmask]> wrote: > Hi again, > > Just resubmitting this question in case anyone can provide any input. > Thank you for your time! > > Warmly, > Erin > > > On Mon, Apr 2, 2018 at 4:01 PM, Erin W. <[log in to unmask]> wrote: > >> Hi all, >> >> I cannot find an answer on previous threads. I have noticed an issue in >> preprocessing where example_func2highres.png file is not generated. >> However, all other example_func2highres files are in the reg directory >> (e.g., .mat, *fast_wmseg) and seem reasonable upon viewing. >> >> Report log specific to example_func2highres is posted below. >> >> For this particular dataset (7T scanner), we have had to use robustfov, >> then bet, to improve skullstripping. >> >> To note, when we use a Freesurfer skull stripped brain as input for the >> main structural, we do not receive any such errors or issue generating the >> .png file. >> >> Thanks for any insight or assistance, >> Erin >> >> ------------- >> Error: >> >> did not find file: example_func2highres.mat. Generating transform. >> >> /nas/longleaf/apps/fsl/5.0.10/fsl/bin/epi_reg --epi=example_func >> --t1=highres_head --t1brain=highres --out=example_func2highres >> Running FAST segmentation FLIRT pre-alignment Running BBR 0.487216 >> 0.998850 -0.030615 0.036900 0.000000 0.030626 0.999531 0.000260 0.000000 >> -0.036891 0.000870 0.999319 0.000000 0.557750 5.505235 -0.433015 1.000000 >> >> /nas/longleaf/apps/fsl/5.0.10/fsl/bin/convert_xfm -inverse -omat >> highres2example_func.mat example_func2highres.mat >> >> >> /nas/longleaf/apps/fsl/5.0.10/fsl/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 ; >> /nas/longleaf/apps/fsl/5.0.10/fsl/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 ; >> /nas/longleaf/apps/fsl/5.0.10/fsl/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 ; >> /nas/longleaf/apps/fsl/5.0.10/fsl/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 ; >> /nas/longleaf/apps/fsl/5.0.10/fsl/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 >> sh: line 1: 29511 Segmentation fault /nas/longleaf/apps/fsl/5.0.10/fsl/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 >> Images aren't the same size! >> >> Cannot open sla.png for reading >> sh: line 1: 29515 Segmentation fault /nas/longleaf/apps/fsl/5.0.10/fsl/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 >> >> Cannot open example_func2highres1.png for reading >> sh: line 1: 29516 Segmentation fault /nas/longleaf/apps/fsl/5.0.10/fsl/bin/pngappend >> example_func2highres1.png - example_func2highres2.png >> example_func2highres.png >> >> >> /bin/rm example_func2highres1.png >> /bin/rm: cannot remove 'example_func2highres1.png': No such file or >> directory >> >> >> >> >