ants Cortical thickness does not complete

[Heiditje]

Hi, using the all in one command, I was able to get FreeSurfer cortical thickness, but ANTs did not complete. Any idea what might be the cause? I am not getting the error message:

Using antsBrainExtraction with the following arguments: image dimension = 3 anatomical image = /home/jovyan/work/S_1OR6QC_T1.nii extraction template = /opt/data/OASIS-30_Atropos_template/T_template0.nii.gz extraction reg. mask = /opt/data/OASIS-30_Atropos_template/T_template0_BrainCerebellumExtractionMask.nii.gz extraction prior = /home/jovyan/work/mindboggle123_output/working/Mindboggle123/antsCorticalThickness/T_template0_BrainCerebellumProbabilityMask.nii.gz output prefix = /home/jovyan/work/mindboggle123_output/ants_subjects/S_1OR6QC_T1.nii/ants output image suffix = nii.gz

N4 parameters (pre brain extraction):
  convergence             = [50x50x50x50,0.0000001]
  shrink factor           = 4
  B-spline parameters     = [200]

Atropos parameters (extraction):
   convergence            = [3,0.0]
   likelihood             = Gaussian
   initialization         = kmeans[3]
   mrf                    = [0.1,1x1x1]
   use clock random seed  = 1

/opt/ants//antsBrainExtraction.sh: line 117: 4124 Killed $cmd Return code: 1 Interface antsCorticalThickness failed to run.

170927-07:03:47,759 workflow INFO:

---

170927-07:03:47,761 workflow ERROR: could not run node: Mindboggle123.antsCorticalThickness 170927-07:03:47,761 workflow INFO: crashfile: /home/jovyan/work/crash-20170927-070347-jovyan-antsCorticalThickness-4803ab36-536a-4b39-8d70-89265c2374f8.pklz 170927-07:03:47,763 workflow INFO:

---

Traceback (most recent call last): File "/opt/conda/bin/mindboggle123", line 311, in mbFlow.run(plugin=args.plugin) File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/workflows.py", line 590, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/plugins/linear.py", line 61, in run report_nodes_not_run(notrun) File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/plugins/base.py", line 101, in report_nodes_not_run raise RuntimeError(('Workflow did not execute cleanly. ' RuntimeError: Workflow did not execute cleanly. Check log for details

Thanks! Heidi

[satra]

@Heiditje - ants is memory hungry and can get killed if it tries to use too much RAM. if you are running through docker, please increase the amount of memory allocated to docker.

if on os x, this is done through the advanced settings under preferences from the docker/whale icon in your status bar.

@binarybottle - in antsCorticalThickness could we use use_floatingpoint_precision=True this will make ants run much faster with much less memory requirements.

[binarybottle]

@satra -- thank you for the pull request #132. Merged, along with the color script, and am now preparing a new, minor release (1.2.2)...