Not sure what is going on. The log file uses 7.3.2, not 7.2.0, at least
on the last invocation. Also, it does not indicate an error on the last
call. If you are running it on a previously existing folder, maybe a
file is there but corrupted.
On 11/26/2024 5:33 PM, Mark Wagshul wrote:
External Email - Use Caution
Hi, I’m hoping someone can help with this strange error. Have been
using recon-all on this dataset forever, and now all of a sudden it is
completely failing just a few minutes into the processing. Attaching
the recon-all.log file (had run a bunch of times, so only saved the
last invocation in the file). It seems to get up to an mris_calc
command to multiply the image by a scaling factor, but the number is
missing.
Here is the last bit of code where it fails:
7.2.0
cwd
cmdline mri_segstats --id 1 --seg
./tmp.mri_nu_correct.mni.1410486/ones.mgz --i
./tmp.mri_nu_correct.mni.1410486/nu0.mgz --sum
./tmp.mri_nu_correct.mni.1410486/sum.junk --avgwf
./tmp.mri_nu_correct.mni.1410486/output.mean.dat
sysname Linux
hostname mwagshul
machine x86_64
user mwagshul
whitesurfname white
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.1410486/ones.mgz
Loading ./tmp.mri_nu_correct.mni.1410486/nu0.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.1410486/output.mean.dat
mri_segstats done
Missing parameters.
Usage:
bc inputImageFile inputSegmentationFile side PathToTrainingFiles
outputSegmentationFile
side = 0 (left side) or else (right side)
*mris_calc -o ./tmp.mri_nu_correct.mni.1410486/nu0.mgz
./tmp.mri_nu_correct.mni.1410486/nu0.mgz mul*
Segmentation fault (core dumped)
Thanks so much in advance for any advice!
Best,
Mark
____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email:_mark.wags...@einsteinmed.edu
<mailto:mark.wags...@einsteinmed.edu>___
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