[Freesurfer] correcting fsaverage surface area by eICV

External Email - Use CautionDear FreeSurfer Developers,   To apply the proportion method to correct for head size for subcortical volumes the volume is divided by the eICV.   To correct for eICV for surface area using the proportion method, is there any problem using mri_concat

Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz

Hi Victor control points are used whenever the white matter intensity is incorrect (>>110 or <<110). If you have regions of white matter that are too bright you should be able to put contgrol points in them to bring the region down. For example, if the gm is so bright that it looks like wm, th

Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz

Hi, Thanks for the clarification. From my understanding, control points are used to grab regions that should be white matter, rather than remove regions that aren't white matter. Are there any resources on how you would use control points to remove intensity inhomogeneity? Victor Zeng Beth Is

Re: [Freesurfer] Threshold values changed/modified before display.

Hi Devavrat freeview definitely does not modify the values in any volumes you load for display. cheers Bruce On Sun, 26 Apr 2020, Devavrat Vartak PhD wrote: External Email - Use Caution Hi freesurfer developers!, I am using Freesurfer 6.0 and the latest (freeview  -beta) t

[Freesurfer] Threshold values changed/modified before display.

External Email - Use Caution Hi freesurfer developers!, I am using Freesurfer 6.0 and the latest (freeview -beta) to display overlays on my flat surfaces. I am a novice user of freesurfer and I am a bit confused with how the overlays are displayed / thresholds calculated. My ov

Re: [Freesurfer] Infant freesurfer

External Email - Use Caution That would be great, thank you! Colleen Pletcher coll...@tpck.net > On Apr 24, 2020, at 3:58 PM, Lilla Zollei wrote: > >  > No, but I can definitely keep you in the loop. > Lilla > >> On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote: >> >> Great, tha

Re: [Freesurfer] exporting segmented mgz file

Hi Atira what was your mri_convert command line? Make sure to specify no scaling of the intensity volume. Can you try adding: -ns 1 to the mri_convert command line, and if that doesn't work send us the full command line and full screen output from it? This is always a good thing to do as it

Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz

Hi Victor the best way to remove intensity inhomogeneities is with control points usually. The wm.mgz gives us an initial estimate of the surface locations, but we then deform it based on the intensities in the brain.mgz volume. So if it looks like wm extends that far out in the brain your wm.