"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 has 3 replies, 5 voices, and was last updated 2 months ago by Anonymous.
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    • #1343
      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.

    • #1800
      umeda-m
      Participant

      I think that the size of the input image is too large.
      When I tried to input 512x512x512 nii files, I encounted the similar error.
      I solved this problem by resizing the input image to 256x256x256.

    • #1806
      Anand Joshi
      Moderator

      Thank you for reporting this.

    • #2133
      Najam
      Participant

      @umeda-m and how to resize image?

    • #2571
      Anonymous
      Inactive

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