[Freesurfer] volume, surface area, and thickness

Dear FreeSurfer experts and developers I am confronted with some technical question of a reviewer. I am not sure about "volume = thickness-by-surface area" and the review's opinion (attached below) about volume, surface area, and thickness was correct. Any comments from FreeSurfer's experts would

Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

No need to rerun anything. It's an issue with the format of those mean path files. Just view them in the standard 5.3 version of freeview for now. On Fri, 26 Aug 2016, Elijah Mak wrote: Hi Anastasia, Yes indeed. I am using a dev version of freeview. I could give it another go with the fre

Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

Hi Anastasia, Yes indeed. I am using a dev version of freeview. I could give it another go with the freeview that came with v5.3. But does this mean that I shoudl also I re-run the tracula -stat on a v5.3? Thanks! Best Wishes, Elijah ___ Freesurfer mai

Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

Hi Elijah - Glad to hear that things worked out! Are you by any chance using the dev version of freeview? a.y On Fri, 26 Aug 2016, Elijah Mak wrote: Hi Anastasia and others, I am trying to visualise the *.path.mean.txt on MNI template after running trac-all -stat. I used this command: fre

Re: [Freesurfer] PET surface sampling

Hi Doug, Thank you. I ran sampled the data and ran mri_glmfit as you suggested, although the resulting bp file seems to only have binary clusters (in the attached image the red cluster all have a value of 1 and everywhere else is 0). Is this the normal output? I expected a more varying map.

[Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

Hi Anastasia and others, I am trying to visualise the *.path.mean.txt on MNI template after running trac-all -stat. I used this command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w stats/*.path.mean.txt However, it looks like something has gone wrong with the labelling and po

Re: [Freesurfer] sig.sum files shows more clusters than sig.mgh image

Dear Doug, I tried using --o instead of --ocp. *Neither the sig.sum nor the sig.mgh file change.* *So i dont see the postcentral cluster neither after running it with --o in sig.mgh.* But the cluster is present in the sig.sum file. i am not sure why it could be like that. Best Georgiana

[Freesurfer] modifying wm.mgz after editing aseg

Dear all my question would be whether editing wm.mgz and running autorecon2-wm will affect a previous edit of aseg? Further can aseg and wm.mgz be processed simultaneously as it is possible for wm.mgz and pial surface using autorecon2-wm? Greetings Julian ___