"out of stack" when running BrainSuite Cortical Surface Extraction

Forums Forums Cortical Surface Extraction "out of stack" when running BrainSuite Cortical Surface Extraction

This topic contains 0 replies, has 1 voice, and was last updated by  snow8080 4 months, 2 weeks ago.

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    snow8080
    Participant

    Hi!
    We once successfully apply Brainsuite for MRI 3T image. However, when we input a higher resolution MRI image, the problem of “out of stack” always happened. We are looking for the solution for this problem.
    Here is the error log we have gotten as follows.
    Could you please help us with it?
    Thanks a lot in advance!

    —- Running BrainSuite Cortical Surface Extraction Sequence —-
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    1. cost(3,25,0.64,1)=1.00006e+06
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    2. cost(3,25,0.64,1)=1.00006e+06
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    3. cost(3,25,0.64,1)=1.00006e+06
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    4. cost(3,25,0.64,1)=1.00006e+06
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    1. cost(3,25.625,0.648,2)=54.7654
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    2. cost(3,25.625,0.648,2)=54.7654
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    3. cost(3,25.625,0.648,2)=54.7654
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    4. cost(3,25.625,0.648,2)=54.7654
    lowest cost(3,25.625,0.648,2)=54.7654
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    Fatal error: out of stack in Graph::visit()
    Stack position is 1000000
    error: illegal code in segment map
    Wrote mask file /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.mask.nii.gz
    Wrote skull-stripped MRI volume /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.bse.nii.gz
    Wrote corrected image /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.bfc.nii.gz
    Wrote tissue label file /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.pvc.label.nii.gz
    Wrote tissue fraction file /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.pvc.frac.nii.gz
    Initializing brain volume
    Performing linear alignment of atlas brain to subject brain
    do_alignlinear.c: 64:
    WARNING: File ‘/fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.air’ will be overwritten by the output of this program
    align.c: 518: WARNING: Registration terminated due to a Hessian matrix that was not positive definite
    Inspection of results is advised
    Performing warp alignment (order=5) of atlas brain to subject brain
    do_align_warp.c: 56:
    WARNING: File ‘/fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.warp’ will be overwritten by the output of this program
    alignwarp.c: 262: WARNING: Registration terminated due to a Hessian matrix that was not positive definite
    Inspection of results is advised
    Labeling brain regions
    Wrote cerebrum mask /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.cerebrum.mask.nii.gz
    Wrote hemisphere label file /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.hemi.label.nii.gz
    Wrote cortex mask file /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.init.cortex.mask.nii.gz
    Iteration: 0 changed: 0
    Wrote output mask /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.cortex.scrubbed.mask.nii.gz
    Largest correction will be 2500
    Fixing topological defects of size 1
    Fixing topological defects of size 21
    wrote surface file /fileserver/projects/3D-EDSR/New3DEDSR/result/1/137128_3T_T1w_MPR1.nii.gz_result.nrrd.inner.cortex.dfs
    /opt/BrainSuite18a/bin/cortical_extraction.sh: line 69: 13119 Segmentation fault (core dumped) ${BrainSuiteBin}pialmesh $VERBOSE -f ${basename}.pvc.frac.$EXT -i ${basename}.inner.cortex.dfs -m ${basename}.cerebrum.mask.$EXT -o ${basename}.pial.cortex.dfs -n 100 -r 1 -s 0.40 -t 1.05 –max 20 –smooth 0.025 –interval 10 –nc 0.2
    cortical extraction halted because pialmesh failed to run or return an error.

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