First of all, do you really need to run the simulation? If you are just
doing a whole hemisphere analysis on fsaverage, then you can use the
precomputed option.

doug

On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote:
> Hi,
>
> I am having problem when running the Monte Carlo script. The script
> seems to fail after only a few simulations but it does not give me any
> error message, it just says 'killed'. I am running it on 126
> participants (2 groups of 63) and I have tried it on a number of
> different measures (sulc, area etc.). I thought it may be an space
> issue but I cleared all other files but that did not seem to make any
> difference.
>
> This is what is printed out on the terminal:
>
> [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15
> --sim mc-z 10000 1.3 mc-z.negative --sim-sign neg --overwrite
>
> cmdline mri_glmfit --y
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods
> --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15
> --surf fsaverage rh --label
> /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat
> --C
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat
>
>
>
> WARNING: unrecognized mri_glmfit cmd option dods
>
>
> SURFACE: fsaverage rh
>
> /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim
>
> --glmdir Rh_JacobianW_15 --sim mc-z 10000 1.3 mc-z.negative --sim-sign
> neg --overwrite
>
> $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $
>
> Thu Apr 24 18:58:31 IST 2014
>
> Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16
> 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux
>
> fitzgeje
>
> setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/
>
> FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0
>
> DoPoll = 0
>
> DoPBSubmit = 0
>
> DoBackground = 0
>
> DiagCluster = 0
>
> gd2mtx = dods
>
> fwhm = 21.770250
>
> nSimPerJob = 10000
>
> 1/1 Thu Apr 24 18:58:31 IST 2014
>
> mri_glmfit --y
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C
> Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx
> --C
> Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx
> --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3
> Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250
> --fsgd Rh_JacobianW_15/y.fsgd dods --label
> /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
> --surf fsaverage rh white
>
> INFO: ignoring tag Creator
>
> INFO: ignoring tag SUBJECTS_DIR
>
> INFO: ignoring tag SynthSeed
>
> reading group avg surface area 822 cm^2 from file
>
> Reading in average area
> /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
>
> reading group avg surface area 822 cm^2 from file
>
> Reading in average area
> /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
>
> simbase Rh_JacobianW_15/csd/mc-z.negative.j001
>
> gdfReadHeader: reading Rh_JacobianW_15/y.fsgd
>
> INFO: demeaning continous variables
>
> Continuous Variable Means (all subjects)
>
> Class Means of each Continuous Variable
>
> 1 groupASD
>
> 2 groupCTRL
>
> INFO: gd2mtx_method is dods
>
> Reading source surface
> /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white
>
> Number of vertices 163842
>
> Number of faces    327680
>
> Total area         65020.765625
>
> AvgVtxArea       0.396850
>
> AvgVtxDist       0.717994
>
> StdVtxDist       0.193566
>
> INFO: fwhm2niters: NOT fixing group surface area
>
> Surface smoothing by fwhm=21.770250, niters=441.000000
>
>
> $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
>
> cwd /projects/pi-lgallagh/HPC_12_00408/qdec
>
> cmdline mri_glmfit --y
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C
> Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx
> --C
> Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx
> --mask Rh_JacobianW_15/mask.mgh --sim mc-z 10000 1.3
> Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250
> --fsgd Rh_JacobianW_15/y.fsgd dods --label
> /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
> --surf fsaverage rh white
>
> sysname  Linux
>
> hostname lonsdale01.cluster
>
> machine  x86_64
>
> user     fitzgeje
>
> FixVertexAreaFlag = 1
>
> UseMaskWithSmoothing     1
>
> fwhm     21.770250
>
> niters    441.000000
>
> OneSampleGroupMean 0
>
> y  /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh
>
> logyflag 0
>
> usedti  0
>
> FSGD Rh_JacobianW_15/y.fsgd
>
> labelmask
>  /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
>
> mask Rh_JacobianW_15/mask.mgh
>
> maskinv 0
>
> glmdir (null)
>
> IllCondOK 0
>
> DoFFx 0
>
> Loading y from
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh
>
> INFO: gd2mtx_method is dods
>
> Matrix condition is 1
>
> /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
> /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
>
> Found 149926 points in label.
>
> Found 149926 voxels in mask
>
> search space = 75188.6
>
> DOF = 124
>
> thresh = 1.3, threshadj = 0.99897
>
>
>
> Starting simulation sim over 10000 trials
>
> Smoothing done, nsteps = 441, tsec = 69.733
>
> Smoothing done, nsteps = 441, tsec = 69.799
>
> Smoothing done, nsteps = 441, tsec = 69.754
>
> Smoothing done, nsteps = 441, tsec = 69.749
>
> Smoothing done, nsteps = 441, tsec = 69.743
>
> Smoothing done, nsteps = 441, tsec = 69.749
>
> Smoothing done, nsteps = 441, tsec = 69.737
>
> Smoothing done, nsteps = 441, tsec = 69.738
>
> Smoothing done, nsteps = 441, tsec = 69.734
>
> Smoothing done, nsteps = 441, tsec = 69.806
>
> Smoothing done, nsteps = 441, tsec = 70.012
>
> Smoothing done, nsteps = 441, tsec = 70.139
>
>
> Killed
>
>
> Any suggestions that may help?
>
> Kind regards,
>
> Jackie
>
>
>
>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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