Thanks again. I will follow the new instructions! 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 4:10:17 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface That one is out of date; we'll delete it. Thanks for pointing it out and sorry for our wiki pointing you in the wrong direction. We're in the process of weeding it out... On 06/09/2016 04:54 PM, Zhao, Yue wrote: > 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 -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
