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 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> 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 --glmdirRh_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.fsgddods
> --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 > > > > > _______________________________________________ > Freesurfer mailing list > 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> 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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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