Hi Doug et al., I indeed found 3 subjects, whose registration looked ok when I eyeballed them with the tkregister 2 command, with values of .9 and higher (all the other subjects had values between .44 and .61). Do you recommend to redo the analysis without them or to run the first level analysis again with --init-spm instead of --init-fsl in bbregister? Also, how is the first value in the .mincost file generated and what does it mean? Can you use this file for other modalities, too? Let's say if I want to do the first level analysis for fct. connectivity instead of PASL for example?
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 6:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation For the range, lower is better, but it impossible to say exactly what is good enough because it depends on your data. If it is 0.8 or higher, then that is probably bad. What I'm hoping is that there will be one or two outliers. The --init-spm was in place of --init-fsl in bbregister. But you only need that if you find a bad registration. On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote: > I checked registration before and it was fine. However, I'll go back and look > at the first value in the aslcal.reg.mincost file. What is the normal range? > Also, I don't understand what you mean with "the FSL initialization fails" > and "try --init-spm" - can you please give me some more information? Thanks! > ________________________________________ > 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 5:21 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Monte Carlo Simulation > > Try checking the individual registrations (or look at the first value in > the .mincost file) to find subjects whose registration may have been off > and so causes the final mask to be non-sense. Sometimes the FSL > initialization fails. If so, you might try it with --init-spm > > > On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote: >> Oh, I see what you mean. I accidentally sent you the within group analysis >> script. I am attaching the first level analysis script now. I also labeled >> the different steps to simplify the script a little bit. >> ________________________________________ >> 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 4:50 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Monte Carlo Simulation >> >> I still can't really tell what it is doing. It looks like it is just >> concatenating several input files that are passed on the command line. >> how were those created? >> >> >> On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote: >>> Sure. I simplified it and attached it again. Please let me know if this is >>> helpful! >>> ________________________________________ >>> 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 3:36 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Monte Carlo Simulation >>> >>> 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 >>> >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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 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 . 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