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> 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 > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > 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 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.
