When you run mri_glmfit, add --mask $SUBJECTS_DIR/fsaverage/mri.2mm/subcort.mask.mgz
doug On 03/13/2015 11:17 AM, Wolthusen, Rick Peter Fritz wrote: > 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 > > -- 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.
