Thanks again! Pedro Rosa.
> On Apr 14, 2016, at 19:25, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 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
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