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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Greg Harris