I'm using version 4.5.0. The --cache does not come up when I type the command mri_glmfit-sim --help?
Best, Jackie On 29 April 2014 16:58, Douglas N Greve <gr...@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 <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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 > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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 > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > 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 > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > > > 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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the > > person to > > > whom it is > > > addressed. If you believe this e-mail was sent to you in > > error and > > > the e-mail > > > contains patient information, please contact the Partners > > > Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent to > > > you in error > > > but does not contain patient information, please contact the > > > sender and properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > -- > > > 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 > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > 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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- 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
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