Hello Bruce,

Thanks for the quick reply. I tried to follow your suggestions, there still seems to be some errors. Hence I am sending you the subject directory, at:

http://www.ensc.sfu.ca/~mfbeg/outgoing/topologyCorrectionProblem_PradeepFrom...

When trying to visualize the defect locations, this is what happened. I also tired running the mris_topo_fixer, but it was complaining that there is no lh.qshere.

Thanks, Pradeep

$ 5:10pm ilpc11: scanner_differences >> tksurfer FirstOrderPoly lh inflated.nofix surfer: current subjects dir: /ensc/grad1/pkr1/UNSW/scanner_differences surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences surfer: Reading header info from /ensc/grad1/pkr1/UNSW/scanner_differences/FirstOrderPoly/mri/T1.mgz surfer: vertices=105340, faces=211208 Loading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/tksurfer.tcl Reading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/tkm_common.tcl Reading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /ensc/IMAGE_MAIN/SOFTWARE/x86_64/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... MRISreadVertexPosition(white): could not open file /ensc/grad1/pkr1/UNSW/scanner_differences/FirstOrderPoly/surf/lh.white No such file or directory % alloc: invalid block: 0x13e04e70: 0 0 65

Abort

On Mon, Mar 2, 2009 at 4:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Pradeep,

sounds like a bug. Can you overlay the surface defect segmentations and see what defect #3 is? If you edit it a bit this will probably go away. If you tar and gzip the subject dir and send it to us we'll take a look You can also try the alternative (newer) topology correction and see if it works properly. Look at the recon-all help for how to run it

cheers Bruce

On Mon, 2 Mar 2009, Pradeep Reddy Ramana wrote:

...

Hello FS Team,

I had a question recently regarding an error encountered in the freesurfer recon-all. I believe error is the result of: mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh

CORRECTING DEFECT 3 (vertices=10731, convex hull=2557) normal vector of length zero at vertex 90051 with 0 faces vertex 90051 has 0 face No such file or directory

recon-all exited with ERRORS

I will appreciate very much if you can suggest a possible fix or a rerun with some set of flags etc.

The partial log and a previous post by somebody else is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09492.html

Thanks, Pradeep