Sorry, I don't have time to deconstruct that script. Can you simplify it for me?
On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote: > This is the script I am using to create cbf.talaraich.mgz (attached). > > Thanks, > Rick > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, March 11, 2015 3:22 PM > To: Freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Monte Carlo Simulation > > Something went very wrong with your first level analysis because the > final mask is pretty messed up. how did you create cbf.talairach.mgz ? > > > On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote: >> 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 >> >> > -- > 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 > > > _______________________________________________ > 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 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.
