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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