No; it is not thickness; it is GM/WM intensity values; thank you for the suggestion with mri_mcsim.
2015-03-23 18:22 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > 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 > -- Dídac Vidal Piñeiro
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