A shell script was used to invoke the following commands on each case:
3dAFNItoMINC Human_Buckner_Case1+orig.HEAD mritotal Human_Buckner_Case1.mnc Human_Buckner_Case1.xfm mincresample -transformation Human_Buckner_Case1.xfm \ -like average_305_mask_1mm.mnc \ Human_Buckner_Case1.mnc mni_Human_Buckner_Case1.mnc
Stripping the node numbers and comments and applying the matrix directly to the triplets works fine, but converting to full-brain grid; applying the matrix; and translating -90,-126,-72 results in an offset between the volume and surface.
tail -3 Human_Buckner_Case1.xfm > Human_Buckner_Case1.mni_mat echo "0 0 0 1" >> Human_Buckner_Case1.mni_mat
head -12 Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.73730.coord > Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.coord
tail +13 Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.73730.coord | cut -f2-4 -d' ' | Vecwarp -matvec Human_Buckner_Case1.mni_mat > Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.triplets
triple_to_coord Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.triplets >> Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.coord
CLOSEDtopo_file Human.sphere_6.LEFT_HEM.73730.topo FIDUCIALcoord_file Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.coord