Hello,<br><br>I&#39;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 &#39;mri&#39; subdirectory (they are also missing the entire surfs directory):<br>


<br>filled.mgz                 <br><div> <br>lh.ribbon.mgz <br>rh.ribbon.mgz<br>ribbon.mgz<br>wm.asegedit.mgz<br>wm.mgz<br>wmparc.mgz<br><br>Below is the last few lines of output from my recon-all log file:<br>
</div><br clear="all">&quot;#@# WM Segmentation Tue Mar 26 18:09:32 EDT 2013<br><br>mri_segment brain.mgz wm.seg.mgz<br><br>doing initial intensity segmentation...<br>using local statistics to label ambiguous voxels...<br>
computing class statistics for intensity windows...<br>WM (104.0): 104.6 +- 4.9 [80.0 --&gt; 125.0]<br>GM (72.0) : 69.4 +- 10.8 [30.0 --&gt; 96.0]<br>setting bottom of white matter range to 80.2<br>setting top of gray matter range to 91.0<br>
doing initial intensity segmentation...<br>using local statistics to label ambiguous voxels...<br>using local geometry to label remaining ambiguous voxels...<br><br>reclassifying voxels using Gaussian border classifier...<br>
<br>removing voxels with positive offset direction...<br>smoothing T1 volume with sigma = 0.250<br>removing 1-dimensional structures...<br>5962 sparsely connected voxels removed...<br>thickening thin strands....<br>20 segments, 3294 filled<br>
117 bright non-wm voxels segmented.<br>4879 diagonally connected voxels added...<br>white matter segmentation took 3.4 minutes<br>writing output to wm.seg.mgz...<br>changing input type from 3 to UCHAR<br><br>mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz<br>
<br>preserving editing changes in input volume...<br>mri_edit_wm_with_aseg: volume brain.mgz must be MRI_UCHAR<br>reading wm segmentation from wm.seg.mgz...<br>Linux <a href="http://ncfc21.rc.fas.harvard.edu">ncfc21.rc.fas.harvard.edu</a> 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<br>
<br>recon-all -s M87190691 exited with ERRORS at Tue Mar 26 18:12:57 EDT 2013<br><br>For more details, see the log file /ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/scripts/recon-all.log<br>
To report a problem, see <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting">http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting</a><br><br>make: *** [/ncf/jwb/studies/PrisonReward/Active/Analyses/fsrecon_n49_01252013_qdec/M87190691/mri/wm.mgz] Error 1&quot;<br>
<br><br>Any ideas as to what might be failing?<br><br><br>Thanks for your help!<br><br>Hayley<br>