mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces
________________________________________ From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: March 25, 2016 6:05 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow what was your mri_glmfit-sim command line? On 03/25/2016 02:00 PM, Miracle Ozzoude wrote: > Hello Bruce and Douglas, > This is what my design looks like. > GroupDescriptorFile 1 > Class Group1 > Class Group2 > Variables Age Firstsessionscore > Input subj1 Group1 72 0.76 > Input subj2 Group1 67 0.43 > Input subj3 Group2 80 1.23 > The contrast matrix i used was [0 0 0 0 0.5 0.5]. I am writing to investigate > if thickness correlates with the score removing the effects of group and age. > The uncorrected map had blue and red colors in some areas of the brain. The > blue color (thickness decreases withe score) seems unlike because i was > expecting all red color(thickness increases with score). After I correcting > for multiple comparison using 3 pos --cwpvalthresh 0.05, I tried to view the > corrected map however, my entire left hemisphere was yellow with no clusters. > how do i fix this?Thanks > Miracle > ________________________________________ > 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: March 24, 2016 6:36 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] whole hemisphere is yellow > > Can you give us more info about the design and the contrast you are > testing? What does the uncorrected map look like? > > On 03/24/2016 09:56 AM, Miracle Ozzoude wrote: >> I used 3 pos --cwpvalthresh 0.05 for correction. This displayed the >> precuneus area in yellow for one of my results however, for the other it >> displayed the entire hemisphere in yellow. Do I need to use the configure-- >> overlay? ‎Also, when I tried to view the cluster summary for the entire >> hemisphere results, I did not see a single cluster unlike, the cluster >> summary for the precuneus results >> >> Sent from my BlackBerry 10 smartphone. >> Original Message >> From: Bruce Fischl >> Sent: Thursday, March 24, 2016 9:48 AM >> To: Freesurfer support list >> Reply To: Freesurfer support list >> Subject: Re: [Freesurfer] whole hemisphere is yellow >> >> >> if it's all yellow it means everything is significant. What threshold are >> you using? >> On Thu, 24 Mar 2016, Miracle Ozzoude wrote: >> >>> Hello Bruce, >>> No. This was after I ran the correction for multiple comparisons. Do I need >>> to change the threshold too? My other results were fine. Thanks >>> Best, >>> Miracle >>> >>> Sent from my BlackBerry 10 smartphone. >>> Original Message >>> From: Bruce Fischl >>> Sent: Thursday, March 24, 2016 8:45 AM >>> To: Freesurfer support list >>> Reply To: Freesurfer support list >>> Subject: Re: [Freesurfer] whole hemisphere is yellow >>> >>> >>> Hi Miracle >>> >>> have you tried changing the thresholds? What kinds of values are you >>> seeing? >>> >>> Bruce >>> On Wed, 23 Mar 2016, Miracle Ozzoude wrote: >>> >>>> hello doug, >>>> i performed a group analysis and after correction for multiple comparisons >>>> when i tried to load the corrected clusters the whole hemisphere was >>>> completely yellow. what should i do? >>>> Best, >>>> Miracle >>>> _______________________________________________ >>>> 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 . 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. >>> >>> >>> _______________________________________________ >>> 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 > > -- 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
