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.wagshul@einsteinmed.edu

 

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