This were the conversations leading up to it "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 -what was your mri_glmfit-sim command line? doug -mri_glmfit-sim --glmdir lh.firstsessionscore1.glmdir --cache 3 pos --cwpvalthresh 0.05 --2spaces miracle -not sure what is happening. Can you tar up the glmfit folder and send it to me at our file drop? doug I just sent it. miracle -What command did you use to visualize? There are no significant clusters so the brain should have been totally blank. doug - this was the command i used "Freeview -f $ SUBJECTS_DIR / fsaverage / surf / lh.inflated -viewport 3d Once I opened freesurfer, I viewed lh.secondsessionscore1.glmdir--> cache.the30.pos.sig.cluster.mgh using the overlay icon ; and lh.secondsessioncore1.glmdir ---> cache.the30.pos.sig.ocn.annot using the annotation icon" Thanks miracle
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: March 28, 2016 6:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] whole brain is yellow
please also include all previous correspondence. We get a lot of emails here and we can't keep track of each person's case, so we have to look at the previous email chain. thanks! doug
On 03/28/2016 02:00 PM, Miracle Ozzoude wrote:
Hello Douglas,
this was the command i used "Freeview -f $ SUBJECTS_DIR / fsaverage / surf / lh.inflated -viewport 3d Once I opened freesurfer, I viewed lh.secondsessionscore1.glmdir--> cache.the30.pos.sig.cluster.mgh using the overlay icon ; and lh.secondsessioncore1.glmdir ---> cache.the30.pos.sig.ocn.annot using the annotation icon"
Thanks
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