Hello Douglas, I just sent you the current file. Thank you. Best, Miracle
________________________________________ From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: March 25, 2016 9:35 PM To: Miracle Ozzoude; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole hemisphere is yellow I meant the glmfit folder, which is lh.firstsessionscore1.glmdir On 03/25/2016 02:29 PM, Miracle Ozzoude wrote: > Hello Douglas, > I have sent the files to you. Thank you. > Best, > Miracle > > ________________________________________ > 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/ > > > -- 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
