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 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.
