the mask was obtained from xjview, and use the MNI space in my study, thanks!
Bo At 2013-06-17 23:52:33,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >sorry, the formatting of your emails is lost in my reader and you may >have said this before, but what is the mask of? What space is it in? > >On Mon, 17 Jun 2013, >xiangbo_2010 wrote: > >> I want to get cortical thickness, and have finished the recon-all, and >> obtained the mask from SPM which include the file with .img and .hdr, >> whether I should convert the file (.img and .hdr) to file (.nii), and use >> the command: "bbregister --s bert --mov func.nii --init-spm --reg >> register.dat tkregister2 --mov func.nii --reg register.dat --surf " to >> obtain the result? thanks! >> >> Bo >> >> >> >> >> >> At 2013-06-17 23:07:19,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >please cc the list so others can answer. Do you mean get cortical >> >thickness? If so, then you need to run recon-all on the structural image >> > >> > >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >wrote: >> > >> >> I have obtained the mask from xjview (.img), I want to obtain the CT from >> >> the mask, thanks! >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >> >what are you trying to map to the surface? >> >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >> >wrote: >> >> > >> >> >> >> >> >> Hi Bruce >> >> >> Thank you for my help, when I use the bbregister, do not know how to c >> hoo >> >> se >> >> >> data for --mov, thanks! >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wro >> te: >> >> >> >Hi Bo, >> >> >> > >> >> >> >tksurfer doesn't take a path to a file. Read the help on it - you nee >> d t >> >> o >> >> >> >reconstrcut the subject with recon-all then give it the subject id. >> To >> >> >> >project a volumetric map onto the surface use mri_vol2surf, with the >> >> >> >registration typically computed by bbregister. >> >> >> > >> >> >> >cheers >> >> >> >Bruce >> >> >> > >> >> >> > >> >> >> >On Mon, 17 Jun 2013, xiangbo_2010 wrote: >> >> >> > >> >> >> >> Hi dougThank you for giving this information, I used the >> >> >> >command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay >> /pa >> >> thn >> >> >> ame/to/s >> >> >> >> pm/roi/yourfile.img/", but do not have results for me, and do not k >> now >> >> ho >> >> >> w >> >> >> >> to do next? thanks! >> >> >> >> >> >> >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-06 23:04:30,"Douglas N Greve" <gr...@nmr.mgh.harvard.edu >> > w >> >> rot >> >> >> e: >> >> >> >> >Hi Stephanie, I don't know which recommendation you are referring >> to. >> >> We >> >> >> >> >> >> >> >get a lot of emails, and I can't remember each one. Can you repost >> wi >> >> th >> >> >> >> >the full thread? >> >> >> >> >doug >> >> >> >> > >> >> >> >> > >> >> >> >> >On 06/06/2013 10:40 AM, McMains, Stephanie wrote: >> >> >> >> >> I am wondering why you didn't tell them to go through fsvarege s >> pac >> >> e? >> >> >> >> >> I thought that was an easy way to go from SPM MNI to freesurfer >> la >> >> nd. >> >> >> >> >> >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pat >> hna >> >> me/ >> >> >> to/ >> >> >> >> spm/roi/yourfile.img/ >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> I am wondering because when I look at the segmentation for fsave >> rag >> >> e, >> >> >> >> >> it seems like it is missing a lot of the gray matter, particular >> ly >> >> in >> >> >> >> >> the big sulci, most likely from the 'smoothing' that comes with >> >> >> >> >> averaging subjects together. And therefore I wonder if this is >> the >> >> >> >> >> >> >> best thing to use as an intermediate step. Are you instead sugg >> est >> >> ing >> >> >> >> >> >> >> >> (as it seemed like in this thread), to put the SPM roi into indi >> vid >> >> ual >> >> >> >> >> >> >> >> subject space and then somehow project it to the surface in free >> su >> >> rfe >> >> >> r? >> >> >> >> >> >> >> >> >> >> Thanks, >> >> >> >> >> Stephanie >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> +++++++++++++++++++++++++ >> >> >> >> >> >> >> >> >> >> Stephanie McMains >> >> >> >> >> Neuroimaging Staff Scientist >> >> >> >> >> Center for Brain Science >> >> >> >> >> Harvard University >> >> >> >> >> 52 Oxford Street >> >> >> >> >> Cambridge, MA 02138 >> >> >> >> >> >> >> >> >> >> +++++++++++++++++++++++++ >> >> >> >> >> For answers to frequently asked questions: >> >> >> >> >> http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/ >> inf >> >> orm >> >> >> ati >> >> >> >> on-investigators/faq >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> >> 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/ >> gre >> >> ve/ >> >> >> >> > >> >> >> >> >_______________________________________________ >> >> >> >> >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 >> who >> >> m i >> >> >> t i >> >> >> >> s >> >> >> >> >addressed. If you believe this e-mail was sent to you in error and >> th >> >> e e >> >> >> -ma >> >> >> >> il >> >> >> >> >contains patient information, please contact the Partners Complian >> ce >> >> Hel >> >> >> pLi >> >> >> >> ne at >> >> >> >> >http://www.partners.org/complianceline . If the e-mail was sent to >> yo >> >> u i >> >> >> n e >> >> >> >> rror >> >> >> >> >but does not contain patient information, please contact the sende >> r a >> >> nd >> >> >> pro >> >> >> >> perly >> >> >> >> >dispose of the e-mail. >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
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