Hi Rick, in the future please post to the list and not to us personally. Thanks! When you did the volume-based analysis, it should have masked out anything anything that was not subcortical. Did it not? If not, then when you run mri_glmfit you can add --mask $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick.
doug On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote: > Hi Doug, > > I was running the following command in launchpad in order to correct > for multiple comparison (using a output file from a PASL FS analysis): > > pbsubmit -m riwohoy -q extended -c "mri_glmfit-sim --glmdir > tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 10000 2.0 > cbf.talairach_p01_abs_montecarlo" > > > When I looked for the surviving clusters, I just found clusters in the > cortical area but not in sub-cortical areas (the cortical clusters > where consistent with the clusters I found in the cortical analyses > though). Is there a way I can limit the Monte Carlo Simulation to > sub-cortical areas only so that I'll also see the most sgn. clusters > in the sub-cortical areas? Please let me know if you have any > additional questions! > > Thanks, > Rick -- 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 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.
