Hi Jürgen,

I have seen this error before. Not sure exactly what is going on. There could be a bug in Han's code, but I could not find it quickly. I don't recommend the rigid alignment in mris_thickness_diff anyway. I have not seen any evaluation on the accuracy of the registration and do not trust it (it is a rigid surface based alignment using the nearest neighbor approach).

Instead try to specify the lta (transform) for the two corresponding volumes. If you use the longitudinal stream, these transforms should be available (either in the <base>/mri/transform or in the <longitudinal-tp>/mri/transform dir). If you are processing your data cross sectionally: I would recommend to do it longitudinally. If that is not an option use mri_robust_register to register the norm.mgz and use that transform for the mris_thickness_diff.

Cheers, Martin

On Mon, 2010-02-08 at 08:30 +0100, Jürgen Hänggi wrote:

Dear FS experts

when running mris_thickness_diff the following error occurred:

mris_thickness_diff \ ? -src_type curv \ ? -out amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness_diff.mgh \ ? -register \ ? -abs -S amblyo_pat01_tp3.long.amblyo_pat01_base1_3 \ ? -L amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh_thickness_diff.log \ ? amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.white \ ? amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.thickness \ ? amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.white \ ? amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness Output differences to file amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness_diff.mgh Do a rigid alignment of two surfaces before mapping to each other logging results to amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh_thickness_diff.log Reading first surface file amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.white Surface1 has 137991 vertices Reading in first data file amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.thickness Reading second surface file amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.white Surface2 has 137991 vertices Reading in second data file amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness Register surface 2 to surface 1 (rigid mapping using ICP)

ERROR: FindClosest: MHTfindClosestVertexNo returned annIndex=-1, which is invalid!

What does it mean?

Thanks in advance Regards Jürgen

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Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)

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