hi after "making final surfaces" i enountered something strange! lh: "inflated" brain and "smoothwm" has no curvature but other surfaces like orig va qshere are normal rh: inflated brain has the curvature but other surfaces are normal logfiles are shown below. what is the prob?!?!? any idea? cheers nimA
FOR LEFT HEMISPHERE "INFLATED":
" env tksurferinterface=csurf patchname= /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/tksurfer -sleep_s2 lh inflated -tcl /tmp/TmpTclSurf.12210 MRISreadVertexPositions(/space/humpback/2/users/nima/csurf/sleep_s2/surf/lhorig): surfaces differ.
No such file or directory MRISreadOriginalProperties: could not read surface file /space/humpback/2/users/nima/csurf/sleep_s2/surf/lh.orig No such file or directory Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkm_wrappers.tcl Using libtclfsgdf.so Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl MRISreadNewCurvature: incompatible vertex number in file /space/humpback/2/users/nima/csurf/sleep_s2/surf/lh.curv surfer: current subjects dir: /space/humpback/2/users/nima/csurf surfer: in subjects "scripts" dir surfer: session root data dir ($session) set to: surfer: /autofs/space/humpback_002/users/nima/csurf/sleep_s2 surfer: /space/humpback/2/users/nima/csurf/sleep_s2/mri/T1/COR-.info surfer: vertices=125362, faces=250720 surfer: using interface /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tksurfer.new.tcl Read /space/lyon/1/home/inverse/freesurfer_alpha/surface_labels.txt, found 95 structures tksurfer: run tcl script: /tmp/TmpTclSurf.12210 surfer: single buffered window surfer: curvature read: min=0.000000 max=0.000000 "
ps. point is that lh.orig exists! so i do not know what it says that it can not find it!
FOR LEFT HEMISPHERE "INFLATED":
"env tksurferinterface=csurf patchname= /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/tksurfer -sleep_s2 lh smoothwm -tcl /tmp/TmpTclSurf.12210 MRISreadVertexPositions(/space/humpback/2/users/nima/csurf/sleep_s2/surf/lhorig): surfaces differ.
No such file or directory MRISreadOriginalProperties: could not read surface file /space/humpback/2/users/nima/csurf/sleep_s2/surf/lh.orig No such file or directory Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkm_wrappers.tcl Using libtclfsgdf.so Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl MRISreadNewCurvature: incompatible vertex number in file /space/humpback/2/users/nima/csurf/sleep_s2/surf/lh.curv surfer: current subjects dir: /space/humpback/2/users/nima/csurf surfer: in subjects "scripts" dir surfer: session root data dir ($session) set to: surfer: /autofs/space/humpback_002/users/nima/csurf/sleep_s2 surfer: /space/humpback/2/users/nima/csurf/sleep_s2/mri/T1/COR-.info surfer: vertices=125362, faces=250720 surfer: using interface /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tksurfer.new.tcl Read /space/lyon/1/home/inverse/freesurfer_alpha/surface_labels.txt, found 95 structures tksurfer: run tcl script: /tmp/TmpTclSurf.12210 surfer: single buffered window surfer: curvature read: min=0.000000 max=0.000000"
ps. point is that lh.orig exists! so i do not know what it says that it can not find it!
FOR RIGHT HEMISPHERE "INFLATED SURFACE": ha/bin/Linux/tksurfer -sleep_s2 rh qsphere -tcl /tmp/TmpTclSurf.12210 mrisReadTriangleFile(/space/humpback/2/users/nima/csurf/sleep_s2/surf/rh.orig): surface doesn't match /space/humpback/2/users/nima/csurf/sleep_s2/surf/rh.qsphere
No such file or directory mrisReadTriangleFile failed.
No such file or directory MRISreadOriginalProperties: could not read surface file /space/humpback/2/users/nima/csurf/sleep_s2/surf/rh.orig No such file or directory Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkm_wrappers.tcl Using libtclfsgdf.so Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl Reading /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl MRISreadNewCurvature: incompatible vertex number in file /space/humpback/2/users/nima/csurf/sleep_s2/surf/rh.curv surfer: current subjects dir: /space/humpback/2/users/nima/csurf surfer: in subjects "scripts" dir surfer: session root data dir ($session) set to: surfer: /autofs/space/humpback_002/users/nima/csurf/sleep_s2 surfer: /space/humpback/2/users/nima/csurf/sleep_s2/mri/T1/COR-.info surfer: vertices=127844, faces=255756 surfer: using interface /space/lyon/1/home/inverse/freesurfer_alpha/lib/tcl/tksurfer.new.tcl Read /space/lyon/1/home/inverse/freesurfer_alpha/surface_labels.txt, found 95 structures tksurfer: run tcl script: /tmp/TmpTclSurf.12210 surfer: single buffered window surfer: curvature read: min=0.000000 max=0.000000"
ps. rh.orig and rh.qsphere exist in surf directory!!!!