Hi Doug et al., Here is the glmdir file you were requesting: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928
Thanks, Rick ________________________________________ From: Wolthusen, Rick Peter Fritz Sent: Tuesday, March 10, 2015 2:10 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: RE: Monte Carlo Simulation Hi FS Community, I emailed with Doug a week ago with regards to limiting the results of a PASL Regression analysis to subcortical areas only in the tal output file (see below). I redid the analysis from scratch adding the flag --mask $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to the above mentioned mask with regards to the used "Mask Vol.". However, the only peak I get after the MCS is still in the cortical area. I am more interested in the subcortical regions though - what else can I do to limit the results to the subcortical regions of interest only? Thanks, Rick ________________________________________ From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, March 02, 2015 4:10 PM To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu Subject: Re: Monte Carlo Simulation 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.
