On 29 April 2014 16:58, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

what version are you using? There is also help when you run
mri_glmfit-sim --help

On 04/29/2014 08:10 AM, Jacqueline Elaine Fitzgerald wrote:
> Hi Doug,
>

> I had not realised that was possible, thanks for that. Will save alot
> of time! I am getting an error that the --cache flag is not
> recognised. This is the command I am running;
>
> [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_thickness_15
> --cache 2.3 neg --cwp 0.05
> ERROR: Flag --cache unrecognized.
>
> Is there an additional directory or step I need to do?
>
> Thanks again for your help,
>
> Best,
>
> Jackie
>
>
>
>
> On 28 April 2014 18:11, Douglas N Greve <greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
> No, I mean using the --cache option which will use precomputed tables
> rather than generating new ones
>
> On 04/24/2014 08:01 PM, Jacqueline Elaine Fitzgerald wrote:
> > Hi Doug,
> >
> > Thank you for your reply. By precomputed do you mean the FDR in the
> > GUI? Apologies I'm still new to the program!
> >
> > I am planning on running an ROI analysis so will need to run it for
> > that anyway (I think?)
> >
> > Best,
> >
> > Jackie
> >
> >
> > On 24 April 2014 21:47, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

> > <mailto:greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> >
> > 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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> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>

> > <mailto:Freesurfer@nmr.mgh.harvard.edu

> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>

> > Phone Number: 617-724-2358 <tel:617-724-2358>

> <tel:617-724-2358 <tel:617-724-2358>>
> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422

> <tel:617-726-7422>>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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> >
> > _______________________________________________
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>

> <mailto:Freesurfer@nmr.mgh.harvard.edu

> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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> >
> >
> >
> >
> > --
> > Jacqueline Fitzgerald
> > PhD Candidate
> > Department of Psychiatry / Trinity Institute of Neuroscience
> > Room 3.36b Lloyd Building
> > Trinity College Dublin
> > Dublin 2
> >
> > Tel: (01) 896 4102
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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>
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>
>
>
>
> --
> Jacqueline Fitzgerald
> PhD Candidate
> Department of Psychiatry / Trinity Institute of Neuroscience
> Room 3.36b Lloyd Building
> Trinity College Dublin
> Dublin 2
>
> Tel: (01) 896 4102
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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--
Jacqueline Fitzgerald

PhD Candidate

Department of Psychiatry / Trinity Institute of Neuroscience

Room 3.36b Lloyd Building

Trinity College Dublin

Dublin 2

Tel: (01) 896 4102