I'm having problems with recon-all. It used to work but recently, every time I've used it, I get a nu_correct error. I don't think we have had any freesurfer upgrades since the last time recon-all worked. Here's the log. Anyone know what's wrong?
ip07:mperry[12] setenv SUBJECTS_DIR <path/to/subjects/dirs> ip07:mperry[13] setenv FUNCTIONALS_DIR <path/to/subjects/dirs> ip07:mperry[14] recon-all -stage1 -subjid subject_ID ######################################## program versions used $Id: recon-all-nmr,v 1.50 2004/08/31 18:05:08 tosa Exp $ $Id: mri_motion_correct2,v 1.8 2004/10/04 22:52:12 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.12 2 003/11/14 16:52:24 stever Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.5.2.1 2003/07/05 01:58:08 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.12 2003/09/18 15:01:33 bert Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6. 4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.11.2.1 2003/11/17 06:01:15 stever Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is <path/to/subjects/dirs> --------------------------------------------- MotionCor Tue Mar 15 16:03:21 PST 2005 <path/to/subjects/dirs>/<subject_ID>/mri/orig mri_motion_correct2 -o . -i 001 -i 002 tmpdir is ./tmp-mri_motion_correct2-23141 -------------------------------------------------------------- mri_motion_correct2 logfile is ./mri_motion_correct2.log -------------------------------------------------------------- ----------------------------------------- Converting 001 Tue Mar 15 16:03:21 PST 2005 mri_convert 001 <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_mo tion_correct2-23141/cor-1.mnc reading from 001... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_ correct2-23141/cor-1.mnc... ----------------------------------------- Converting 002 Tue Mar 15 16:03:29 PST 2005 mri_convert 002 <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_mo tion_correct2-23141/cor-2.mnc reading from 002... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_ correct2-23141/cor-2.mnc... ----------------------------------------- Motion Correcting <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_ motion_correct2-23141/cor-2.mnc Tue Mar 15 16:03:36 PST 2005 COG of v1: 2.191772 14.916920 -47.842663 COG of v2: 2.203371 14.932534 -47.776924 [trans] = 0.011599 0.015615 0.065739 Initial objective function val = 0.01807109 Final objective function value = 0.00892547 ----------------------------------------- Resampling <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_ correct2-23141/cor-2.mnc Tue Mar 15 16:04:30 PST 2005 Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done ----------------------------------------- Averaging Tue Mar 15 16:04:37 PST 2005 Processing:..................................................................... ................................................................................ ................................................................................ ...........................Done ----------------------------------------- Converting Average to output Tue Mar 15 16:04:41 PST 2005 mri_convert <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion _correct2-23141/avgvol.mnc . -tr 2730 -te 3.31 -TI 1000 -flip_angle 0.122173 reading from <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motio n_correct2-23141/avgvol.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to .... Started at: Tue Mar 15 16:03:21 PST 2005 Ended at: Tue Mar 15 16:04:46 PST 2005 mri_motion_correct2: done --------------------------------------------- Nu Intensity Correction Tue Mar 15 16:04:46 PST 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mperry@ip07:<path/to/subjects/dirs>/<subject_ID>/mri/] [2005-03-15 16:0 4:54] running: /usr/pubsw/packages/mni/1.2/bin/nu_estimate_np_and_em -parzen -log -sharpen 0. 15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -d istance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_2326 4/ nu0.mnc nu1.imp
spawn: exec of sharpen_volume failed: No such file or directory nu_estimate_np_and_em: crashed while running sharpen_volume (termination status= 65280) nu_correct: crashed while running nu_estimate_np_and_em (termination status=6528 0) ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on
693727248 307742336 350745536 47% /space/aliens/1 ------------------------------------------ recon-all exited with errors at Tue Mar 15 16:04:55 PST 2005