14 Apr
2016
14 Apr
'16
6:25 p.m.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
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MGH-NMR Center
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