Hi
I emailed a little while ago about this, but I haven't heard any solutions yet. As a check, I re-ran recon-all again this morning on a local machine. Still crashing. Here is the output:
recon-all -s $SUBJECT -motioncor
INFO: SUBJECTS_DIR is /autofs/space/megraid_043/seder/freesurfer Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev -rw-rw-r-- 1 dwakeman megclin 27336 Mar 10 18:01 /autofs/space/megraid_043/seder/freesurfer/nmr00069/scripts/recon-all.log Linux rerun 2.6.9-22.0.2.106.unsupportedsmp #1 SMP Fri Jan 20 04:48:30 CST 2006 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Thu Mar 23 11:37:22 EST 2006 Found 2 runs /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz #----------------------------------------------- /autofs/space/megraid_043/seder/freesurfer/nmr00069
mri_motion_correct.fsl -o /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/rawavg.mgz -wild /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz
tmpdir is /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz Thu Mar 23 11:37:32 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069 mri_convert /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img -odt float reading from /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz... TR=2000.00, TE=3.25, TI=950.00, flip angle=7.00 i_ras = (-0, -1, -5.55112e-17) j_ras = (-0.0401318, -0, -0.999194) k_ras = (-0.999194, -0, 0.0401318) changing data type from 4 to 3 (noscale = 0)... writing to /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img... Analyze Output Matrix -0.000 -0.040 -0.999 91.684; -1.000 -0.000 -0.000 129.675; -0.000 -0.999 0.040 117.569; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz Thu Mar 23 11:37:37 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069 mri_convert /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img -odt float reading from /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz... TR=2000.00, TE=3.25, TI=950.00, flip angle=7.00 i_ras = (-0, -1, -5.55112e-17) j_ras = (-0.0401318, -0, -0.999194) k_ras = (-0.999194, -0, 0.0401318) changing data type from 4 to 3 (noscale = 0)... writing to /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img... Analyze Output Matrix -0.000 -0.040 -0.999 91.684; -1.000 -0.000 -0.000 129.675; -0.000 -0.999 0.040 117.569; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img Thu Mar 23 11:37:43 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069 fsl_rigid_register -maxangle 90 -r /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img -i /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img -o /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img -tmpdir /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Thu Mar 23 11:37:43 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /autofs/space/megraid_043/seder/freesurfer/nmr00069 calling eval flirt -in /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.hdr -out /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.hdr -omat /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image
Started at Thu Mar 23 11:37:43 EST 2006 Ended at Thu Mar 23 11:43:33 EST 2006
fsl_rigid_register Done
To check results, run: tkmedit -f /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img -aux /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img
mv /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img ----------------------------------------- Averaging Thu Mar 23 11:43:33 EST 2006 /autofs/space/megraid_043/seder/freesurfer/nmr00069 inhibiting isotropic volume interpolation 1 of 2: reading /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img... 2 of 2: reading /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img... INFO: analyzeRead(): min = 0, max = 1543 ERROR: premature end of file ERROR: Success (0) frame = 0, slice = 158, k=158, row = 0 nread = 0, nexpected = 256 fname = height = 256 width = 256 depth = 160 nframe = 1 imnr0 = 1 imnr1 = 160 xnum = 256 ynum = 256 fov = 256.000000 thick = 1.000000 xstart = -128.000000 xend = 128.000000 ystart = -128.000000 yend = 128.000000 zstart = -80.000000 zend = 80.000000 type = 3 xsize = 1.000000 ysize = 1.000000 zsize = 1.000000 x ras = 0.000000 -1.000000 -0.000000 y ras = -0.040132 0.000000 -0.999194 z ras = -0.999194 0.000000 0.040132 c ras = 5.572693 0.674698 -8.076317 det(xyz_ras) = -1.000000 ras_good_flag = 1 brightness = 1 subject_name = path_to_t1 = fname_format = analyzeRead2(): error reading from file /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img mri_average: MRIread(/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img) failed Linux rerun 2.6.9-22.0.2.106.unsupportedsmp #1 SMP Fri Jan 20 04:48:30 CST 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Thu Mar 23 11:43:38 EST 2006