Yes, 35 is more than I've precomputed. But another question is whey it is 35 when it looks like you've smoothed it by only 15. What is the nature of this data? Is it thickness?
If this is something you really need/want to do, I'm recommending that people start using mri_mcsim instead of running the simulation from mri_glmfit-sim http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo On 03/23/2015 01:14 PM, Dídac Vidal wrote: > Yes, > > the mri_glmfit run correctly (also for a similar analysis where the > computed FWHM was under 30 mri_glmfit-sim run without problems) > > the mri_glmfit command was: > /mri_glmfit --glmdir $path/resultsDIR --y > $path/lh.all_long.wm_orig_0.2.mgh-rate.fwhm15.fsaverage.mgh --fsgd > $path/gender_csf_stroop4th_rate.fsgd --C $path/Stroop_simple.mtx --C > $path/CTh_simple.mtx --surf fsaverage lh --pvr > $path/lh.all_long.thickness.mgh-rate.fwhm15.fsaverage.mgh/ > > I used the simulation because when I used cached data, I got this > following error: > /mri_glmfit-sim --glmdir $path/resultsDIR --cache 2.3 abs --2s > paces/ > > /(...) > fwhm = 35.068253 > ERROR: cannot find > $path/freesurfer/freesurfer.5.3.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/abs/th23/mc-z.csd/ > > > I thought that the main the reason why it failed was that computed > fwhm was more than the maxium cached in freesurfer. > > Thank you very much again. > > 2015-03-23 17:36 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > > > did this run correctly with just mri_glmfit? What was your mri_glmfit > command line? Why are you running a simulation instead of using > cached data? > > doug > > On 03/21/2015 10:52 AM, Dídac Vidal wrote: > > Dear Freesurfer users, > > > > I am trying to run mri_glmfit in simulation mode as the computed > FWHM > > is over 30 > > > > I run --> mri_glmfit-sim --glmdir GLMDIR > > \--sim mc-z 10000 1.3 mc-z.abs.13 > > \--sim-sign abs > > > > However I get an dimension mismatch error > > > > --> ERROR: dimension mismatch between X and contrast > [...] X > > has 6 cols, C has 7 cols > > > > Significantly the model included one per-vertex regressor (which is > > the main reason why *mtx files have 7 cols) > > > > > > Does anybody know how to solve this problem? > > Should I create an extra column in the matrix? > > > > Thank you very much in advance > > > > -- > > Dídac Vidal Piñeiro > > > > > > _______________________________________________ > > 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 > > > 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. > > > > > -- > Dídac Vidal Piñeiro > > > _______________________________________________ > 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
