Confirmed. All inputs exist, have the correct folder and file names, and there are no permissions problems. I'm getting this on several datasets, for example:
/gmrrc/mrbin/fsl.cver/bin/fslmaths /oxford/jlsmith/RSFMRI/mtbi/05-03-091E-044_SG_time2/20100120_111656IM_0016T2WTSEAXCSENSEEINSTEINResearchs801a1008 initial_highres
/gmrrc/mrbin/fsl.cver/bin/fslmaths /oxford/jlsmith/RSFMRI/mtbi/05-03-091E-044_SG_time2/20100120_111656IM_0005T1W3DTFESSENSEEINSTEINResearchs301a1003 highres
/gmrrc/mrbin/fsl.cver/bin/fslmaths /oxford/jlsmith/RSFMRI/mtbi/05-03-091E-044_SG_time2/20100120_111656IM_0005T1W3DTFESSENSEEINSTEINResearchs301a1003 highres_head
/gmrrc/mrbin/fsl.cver/bin/fslmaths /gmrrc/MODELS/human_mni_jhu_t1_brain standard
Error: you have not selected any images to register to!
I get the same error no matter what: I've tried copying the template to my own directory and also specifying the output directory name explicitly (it defaults to <SubjectFolder>/. -- i.e., <SubjectFolder>/.feat, a hidden directory -- when the subject directory is selected, and I thought that might be the culprit. It wasn't).
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