Hi All,


I am not sure if the question is successfully posted. If the post is there, does anyone has any idea? Thanks a lot!


Yue

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zhao, Yue <zhao.y@wustl.edu>
Sent: Tuesday, June 07, 2016 4:15:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Resampling the parametric map of brain activations onto a surface
 

Hi All,


I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying to overlay a parametric map onto a FreeSurfer surface. Here are the tutorial codes I found:

1. To resample the paramatric map onto the individual's surface:

mri_vol2surf --src spm001.img  --srcreg register.dat --hemi lh --projfrac 0.5 --out ./spm001-lh.w --out_type paint
2. Visualize and overlay: 

qsurfer -stat spm001 -hemi lh -subject bert-brf
3. Configure the image by selecting "View -> Configure -> Overlay" and play with the histogram


The image looks like this:


I assigned one single value to the voxels in each cortical parcellation. So the white matter and subcortical regions (e.g. caudate, putamen, hippocampus) are 0. The contrast represents the variations of the parameter across the cortex. Everything looks good to me except that I couldn't get rid of that green "noise" appearing at the hippocampus and occipital area. Does anyone have any idea why this is happening and how to get rid of it?


Another minor issue is that even though I play with the histogram in "Overlay" to get the best contrast, the colorbar looks less dynamic. Too much red but very little yellow. Any suggestion to improve that?


Thanks a lot! 


Best,

Yue