You will need to also specify a voxel-wise threshold and sign, eg, --cache 2 abs
On 04/13/2016 07:37 PM, Pedro Rosa wrote: > Thanks, Doug. > When I do it, I get the following error: ERROR: must spec --sim > I am using FreeSurfer 5.3 in a Mac OS. I read in the wiki that > mri_mcsim got an atualization for Linux. Should I get that > atualization for Mac Os? > Best, > Pedro. > > On Wed, Apr 13, 2016 at 11:43 AM, Douglas Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Try it without the --no-sim. The --no-sim was from before I stored > the cached data and you either had to run a simulation or not. > > > On 4/12/16 9:10 PM, Pedro Rosa wrote: >> Dear list, >> I want to limit my vertex-wise group analysis to a smaller >> spatial region, then I ran my own Monte-Carlo simulation on >> fsaverage for the superior temporal gyrus: >> >> mri_mcsim --o lh/superiortemporal --base mc-z --surface >> /fsaverage lh --nreps 10000 --label superiortemporal >> >> >> After 36 hours, it finished and I pasted the resulting into >> $FREESURFER_HOME/average/mult-comp-cor/fsaverage, and ran glmfit: >> >> mri_glmfit --glmdir glmdir --y lh.thickness.5.mgh --fsgd >> table.fsgd --C contrast.mtx --surface fsaverage lh --label >> /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label >> >> It seems it ran only on the label, as expected. >> >> However I am not able touse this pre-cached simulation in >> mri_glmfit-sim. >> >> I tried: mri_glmfit-sim --glmdir glmdir --sim-sign abs >> --cache-dir >> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/superiortemporal >> --no-sim mc-z.abs.th13 --cache-label >> /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label >> >> >> ...but I get an error although the csd files are in >> /average/mult-comp-cor/fsaverage... path : ERROR: cannot find any >> csd files >> >> I tried several combinations of the text specified after >> --no-sim, but all I got is the error above. I though I should >> refer to my own simulation using --cache-dir, but it requires the >> --no-sim flag. >> >> Can anyone help me? >> >> Best, >> >> Pedro Rosa. >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > 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. > > > > > _______________________________________________ > 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
