Hello, I am trying to use Xiao Han's ThicknessRepeatability methods for a longitudinal study. I have successfully completed step one, which is rigid registration of the pre and post scans, but I am having problems with step 2. This step uses the mris_thickness_diff function to compute the thickness difference map. I use the following command, as suggested by Xiao Han:
mris_thickness_diff -xform $SUBJECTS_DIR/1001/mri/transforms/1001_to_1001a.lta \ -src_type curv \ -out $SUBJECTS_DIR/1001/surf/lh.thickness_diff.mgh \ -nsmooth 0 \ -abs -S 1001 \ -L $SUBJECTS_DIR/1001/surf/lh_thickness_diff.log \ $SUBJECTS_DIR/1001/surf/lh.white \ $SUBJECTS_DIR/1001/surf/lh.thickness \ $SUBJECTS_DIR/1001a/surf/lh.white \ $SUBJECTS_DIR/1001a/surf/lh.thickness The function successfully reads the surfaces, but if fails when trying to apply the LTA xform to align surface 1 to surface 2. The terminal states: INFO:try to get src info from transform. ERROR: ComputeDifferenceNew: MHTfindClosestVewrtexNo returned nnindex=-1, which is invalid I have experienced this error for multiple subjects and have been unable to get past it. I am unsure of what the nnindex is and why it is -1. Any help on this issue would be greatly appreciated. Thanks. -Scott Beeman
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