Hi Douglas, This is the instruction I am using. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FuncOverlay
I cannot insert the picture in this email. I attach it. Hope it helps. Thanks very much! Yue ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Thursday, June 09, 2016 3:38:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface Sorry for the delay. I can't see the image. Also, what instructions are you following? They look pretty old. check out our multimodal tutorial instead https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview On 06/09/2016 10:19 AM, Zhao, Yue wrote: > > 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: > > > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
_______________________________________________ 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.
