also, i do require a username and password in order to send you the folder.
________________________________________ From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: March 25, 2016 6:11 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow not sure what is happening. Can you tar up the glmfit folder and send it to me at our file drop? https://gate.nmr.mgh.harvard.edu/filedrop2 On 03/25/2016 02:09 PM, Miracle Ozzoude wrote: > 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/ > > > -- 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
