I am running under Redhat 4. This occurs on both 32-bit and 64-bit Intel architecture processors. I began it this way:
recon-all -subjid IowaFifty_2005_0182497 -autorecon3 -hemi lh
It began this way...
INFO: SUBJECTS_DIR is /IPLlinux/raid0/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects Actual FREESURFER_HOME /opt/freesurfer_20060304_4x86_64 -rw-rw-r-- 1 harris prog 796047624 Mar 20 14:46 /IPLlinux/raid0/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0182497/scripts/recon-all.log Linux chiarugi.psychiatry.uiowa.edu 2.6.9-22.0.2.EL #1 Thu Jan 5 17:03:08 EST 2006 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Sphere lh Mon Mar 20 14:46:53 CST 2006 /IPLlinux/raid0/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0182497/scripts
mris_sphere ../surf/lh.inflated ../surf/lh.sphere
$Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ $Id: mrisurf.c,v 1.441 2006/02/24 20:40:56 fischl Exp $ reading original vertex positions... MRISreadVertexPosition(smoothwm): could not open file ../surf/lh.smoothwm No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory unfolding cortex into spherical form... surface projected - minimizing metric distortion... tol=5.0e-01, host=chiar, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization
so looking backward in my logs, I found that the autorecon2 didn't finish successfully. I guess I'll just re-run it tonight. Thanks anyway.
Greg
Bruce Fischl wrote:
Hi Greg,
this isn't nearly enough information for us to track it down. What binary is failing? What version? What hardward/os? Please be more detailed.
Bruce
On Mon, 20 Mar 2006, Greg Harris wrote:
In a sample of 50 brains, I found two hemispheres that fail at autorecon3, printing a whole lot of this:
zero distance at v 91420, n 0 (vn = 89897) zero distance at v 91420, n 1 (vn = 91419) zero distance at v 91420, n 2 (vn = 91421) zero distance at v 91420, n 3 (vn = 91402) zero distance at v 91420, n 4 (vn = 88463) zero distance at v 91420, n 5 (vn = 89896) zero distance at v 91420, n 6 (vn = 88475) zero distance at v 91420, n 7 (vn = 89912) zero distance at v 91420, n 8 (vn = 91401) zero distance at v 91420, n 9 (vn = 89913) zero distance at v 91420, n 10 (vn = 91438) zero distance at v 91420, n 11 (vn = 91404) zero distance at v 91420, n 12 (vn = 91422) zero distance at v 91420, n 13 (vn = 92898) zero distance at v 91420, n 14 (vn = 92899) zero distance at v 91420, n 15 (vn = 91384) zero distance at v 91420, n 16 (vn = 91385) zero distance at v 91420, n 17 (vn = 92900) zero distance at v 91420, n 18 (vn = 92900) zero distance at v 91420, n 19 (vn = 92900) zero distance at v 91420, n 20 (vn = 92898) zero distance at v 91420, n 21 (vn = 91439) zero distance at v 91420, n 22 (vn = 91384) zero distance at v 91420, n 23 (vn = 92881) zero distance at v 91420, n 24 (vn = 91404) zero distance at v 91420, n 25 (vn = 89899) zero distance at v 91420, n 26 (vn = 91400) zero distance at v 91420, n 27 (vn = 88462) zero distance at v 91420, n 28 (vn = 89882) zero distance at v 91420, n 29 (vn = 91440) zero distance at v 91420, n 30 (vn = 88485) zero distance at v 91420, n 31 (vn = 91385) zero distance at v 91420, n 32 (vn = 89884) zero distance at v 91420, n 33 (vn = 88474) zero distance at v 91420, n 34 (vn = 89928) zero distance at v 91420, n 35 (vn = 88449) zero distance at v 91420, n 36 (vn = 88496) zero distance at v 91420, n 37 (vn = 88486) zero distance at v 91420, n 38 (vn = 89885) zero distance at v 91420, n 39 (vn = 88450) zero distance at v 91420, n 40 (vn = 89869) zero distance at v 91420, n 41 (vn = 91474) zero distance at v 91420, n 42 (vn = 91441) zero distance at v 91420, n 43 (vn = 86953) zero distance at v 91420, n 44 (vn = 89852) zero distance at v 91420, n 45 (vn = 88451) zero distance at v 91420, n 46 (vn = 86952) zero distance at v 91420, n 47 (vn = 92853) zero distance at v 91420, n 48 (vn = 89942) zero distance at v 91420, n 49 (vn = 88414) zero distance at v 91420, n 50 (vn = 86929) zero distance at v 91420, n 51 (vn = 91473) zero distance at v 91420, n 52 (vn = 89867) zero distance at v 91420, n 53 (vn = 92928) zero distance at v 91420, n 54 (vn = 89939) zero distance at v 91420, n 55 (vn = 91443) zero distance at v 91420, n 56 (vn = 91476) zero distance at v 91420, n 57 (vn = 86928) zero distance at v 91420, n 58 (vn = 88494) zero distance at v 91420, n 59 (vn = 86973) zero distance at v 91421, n 0 (vn = 89898) zero distance at v 91421, n 1 (vn = 91420) etc. etc.
Any idea where to look for the cause of this bug? I discovered it because these hemispheres are missing their [lr]h.smoothwm, although they have [lr]h.smoothwm.nofix files.
( for my reference, they are the left hemisphere of scan 0182497 and the right hemisphere of scan 0193095.)
Greg Harris
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