Hi,

I'm working with the recon-all -long processing stream. It went all the way through on one of my brains yesterday, but today it's stopping around here:

____________________________________________ invert the first LTA before applying it Talairach xfrm src file is /space/jizo/1/users/STRUCTURALS/MBSR/MS2-09M_prereconEDIT/mri/orig.mgz Talairach xfrm dst file is /usr/local/freesurfer/stable/mni/bin/../share/mni_autoreg/average_305.mnc INFO: dst volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (172, 220, 156) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : ( 1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 1.0000, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.0950, -16.5100, 9.7500) file : /usr/local/freesurfer/stable/mni/bin/../share/mni_autoreg/average_305.mnc volume geometry: extent : (86, 110, 68) voxel : ( 2.0000, 2.0000, 2.0000) x_(ras) : ( 1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 1.0000, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.0950, -16.5100, 9.7500) file : /usr/local/freesurfer/stable/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 7.4766, 9.4936, -0.2721) file : /space/jizo/1/users/STRUCTURALS/MBSR/MS2-09M_prereconEDIT/mri/orig.mgzvolume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 7.4766, 9.4936, -0.2721) file : /space/jizo/1/users/STRUCTURALS/MBSR/MS2-09M_prereconEDIT/mri/orig.mgzRead individual LTAs Warning: dst volume of lta1 doesn't match src volume of lta2 Volume geometry for lta1-dst: Volume geometry for lta2-src: Combine the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2 xfma: Undefined variable. jizo:ccongle[116] _________________________________________________________

I'm not sure what the 'xfma' is. Do you know what the problem might be?

Thanks, Christina