Hi everyone, I met some problems when I tried to do surface registration on my own monkey dataset with F99 atlas according to FS-to-F99 tutorial. According to the tutorial, I adjusted my volume from LIA orientation to LPI orientation by mri_convert --in_orientation LPI. However, I failed to well-align my surface with my volume in CARET when I loaded WW.R.Stage-1.spec. In FreeSurfer, the surface and the volume can be in register, while in CARET they seem to share different origin and orientation. I also tired to convert the original volume orientation to RAS, but it still failed. Besides that, I found the deform_map file had a wrong name, i.e. F99-registered..WW.R.For-Reg-with-F99.74k_f99.deform_map, double dot before the case name WW. The deform_map is created by caret_command -surface-register-sphere-spec-only N $ATLAS_DIR/Macaque.TEMPLATE.FS-to-F99.LVD.deform_map $CASE.$HEM_FLAG.For-Reg-with-F99.$NUMBER_NODES.spec $ATLAS_DIR/Macaque.F99.R.For-Registration-with-$CASE.$HEM_FLAG.74k_f99.spec
in Stage 3. Another error occured in the subsequent caret_command -surface-distortion Macaque.ATLAS.sphere.6.74k.coord WW.R.SPHERICAL_STD.74k_f99.coord Macaque.sphere_6.RIGHT_HEM.74k.topo WW.R.74k_f99.surface_shape WW.R.74k_f99.surface_shape -generate-areal-distortion -areal-distortion-column-name "Spherical distortion deformed WW.R vs F99.R sphere" with "BrainSet construction error: Expected '>' or '/', but got '[0-9]' " and "SURFACE DISTORTION ERROR: unable to find second surface." Does anyone has any suggestion to fix these things? Thank you very much! Zhuangming
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