yes, assuming you ran mri_glmfit with that label as a mask On 04/14/2016 06:06 PM, Pedro Rosa wrote: > Hi, > Many many thanks. It worked: > > mri_glmfit-sim --glmdir teste2 --cache-dir > /$FREESURFER_HOME/average/mult-comp-cor/ --cache 1.3 abs --cache-label > superiortemporal > > I had so specify --cache-label as well, or it would try to find the > default fsaverage/cortex label. > > The summary table is named as the deafault ones > (cache.th13.abs.sig.cluster.summary), but I found this in it: > > # SearchSpace_mm2 65416.6 ## against 65020.8 for deafult ones > > # SearchSpace_vtx 7271 ## against 149926 for default ones > > Does this mean that both GLM and Monte-Carlo ran in the label > exclusively? By the way, no cluster survived the correction. > > Best, > > Pedro. > > > On Thu, Apr 14, 2016 at 6:49 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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> > <mailto: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> > >> <mailto: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> > <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. > > > > > > > > > > _______________________________________________ > > 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 > > > > > _______________________________________________ > 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
