Hi Hayley
I think the problem is that the nu.mgz I gave you has a voxel type of
float (3) instead of uchar (0). You will need to figure out which volumes
are float with mri_info, and convert each of them to uchar with:
mri_convert -odt uchar -ns 1 float.mgz uchar.mgz
where the -ns 1 flag tells it not to scale the intensities. Sorry, I
should have thought of this before sending you the updated nu.mgz. Make
sure all the uchar volumes are named as we expect them
Bruce
On Wed, 27 Mar 2013, Hayley Dorfman wrote:
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
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