Hello,
I've been having problems with recon-all for only 1 of my 50 subjects. Recon-all is failing somehow before white matter or surf files are generated. The T1 and nu.mgz files look fine. Below are the files that my subject is missing in the 'mri' subdirectory (they are also missing the entire surfs directory):
filled.mgz
lh.ribbon.mgz rh.ribbon.mgz ribbon.mgz wm.asegedit.mgz wm.mgz wmparc.mgz
Below is the last few lines of output from my recon-all log file:
"#@# WM Segmentation Tue Mar 26 18:09:32 EDT 2013
mri_segment brain.mgz wm.seg.mgz
doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.6 +- 4.9 [80.0 --> 125.0] GM (72.0) : 69.4 +- 10.8 [30.0 --> 96.0] setting bottom of white matter range to 80.2 setting top of gray matter range to 91.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5962 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3294 filled 117 bright non-wm voxels segmented. 4879 diagonally connected voxels added... white matter segmentation took 3.4 minutes writing output to wm.seg.mgz... changing input type from 3 to UCHAR
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
preserving editing changes in input volume... mri_edit_wm_with_aseg: volume brain.mgz must be MRI_UCHAR reading wm segmentation from wm.seg.mgz... Linux ncfc21.rc.fas.harvard.edu 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s M87190691 exited with ERRORS at Tue Mar 26 18:12:57 EDT 2013
For more details, see the log file /ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
make: *** [/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/mri/wm.mgz] Error 1"
Any ideas as to what might be failing?
Thanks for your help!
Hayley