Ok! Can I still use these masks as long as I know what areas are interpretable? If so, what does it mean in terms of my original question (limiting the MCS to subcortical structures)? ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 12, 2015 10:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation
Yes, that probably is the reason. doug On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote: > To be honest, I checked the between subject alignment and it looked pretty > good. None of my subjects was way out of alignment. However, since we cannot > fit the whole brain in the slice during scanning, we are always cutting of > the top of the brain, sometimes more, sometimes less, depending on the brain > size. Could this be the reason why the mask is off? If not, is there anything > else I can check? > ________________________________________ > 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: Thursday, March 12, 2015 2:47 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Monte Carlo Simulation > > I meant which ones are causing the problems when you run mri_glmfit. > When you run fslview you will see something that looks like a brain. As > you scroll thru the different time points, you'll see the CBF maps for > different subjects. They should be more-or-less in alignment. Look for > ones that are way out of alignment or don't have all of the brain. > > On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote: >> Well, I checked the proper match of ASL and anatomical scans again and one >> of the subjects I reported before was indeed wrongly matched. Thanks! >> >> What do you mean with "So the next thing I would do is to find which >> subjects are the >> ones that are off."? You mean off when I check for registration? That's what >> I did before with tkregister2 and they all looked fine to me. What do I look >> for when I open the cbf.talaraich.nii.gz file in fslview? >> ________________________________________ >> 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: Thursday, March 12, 2015 12:19 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Monte Carlo Simulation >> >> If the registration looks ok, then that is all that counts. However, I'm >> a bit sceptical that the reg looks ok but the mincost is that much >> different than the others. You should double check that the ASL is >> properly matched with the corresponding anatomical (ie, it is not two >> different subjects). This would also not explain why the masks were so >> far off. So the next thing I would do is to find which subjects are the >> ones that are off. You can do this with something like >> >> fslview y.nii.gz >> >> where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit >> (you can mri_convert it to nii.gz). You can then step through each frame >> (or play them as a movie) to see if any look odd. >> >> The mincost is from the BBR cost function. It is basically the mean >> gray/white contrast across cortex passed through a sigmoid function to >> make its range 0-1, 0 being best. You cannot necessarily generalize the >> normal range for one modality to that of another. >> >> >> On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote: >>> 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 >>> >>> >> -- >> 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 > > _______________________________________________ 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. 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