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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zhao, Yue <zha...@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: [https://mail.google.com/mail/u/0/?ui=2&ik=fffa1c9b37&view=fimg&th=1552b8aa077ac979&attid=0.1&disp=emb&attbid=ANGjdJ-pqlhFTJE2srxoou8y6c01tMI8Eewf-ICJtNACyUAHlD_817oQYfKULQ9ELG6ujIbOeI4-BaiWb8MEYUJrNVc1_0eYQdj5aeC2OAw5GYoPb0BPNmTWuB9yEck&sz=s0-l75-ft&ats=1465314364876&rm=1552b8aa077ac979&zw&atsh=1] 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
_______________________________________________ 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.
