Hi Zhuangming, The orientation issue needs sorting, because downstream things will fail if that's not right. Upload the volume to which your surface is aligned here:
http://brainvis.wustl.edu/cgi-bin/upload.cgi I may not be able to look at it until tomorrow, but someone else might get a chance sooner. I thought perhaps the double dot in the filename might result from a missing variable setting, but the CASE and HEM_FLAG variables appear to be set and resolving. From this, I infer that a dot or two might be specified in the template deform map file, in the prefix field. I'm not familiar with this tutorial or its dataset, but try this: grep -a prefix $ATLAS_DIR/Macaque.TEMPLATE.FS-to-F99.LVD.deform_map Is there a dot or two in the prefix setting? The distortion error stumps me. Donna On Jul 19, 2013, at 10:30 PM, 沈庄明 wrote: > 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 $ATLAS_DIR/M > acaque.F99.R.For-Registration-with-$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 > > > > > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
