I 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 choo >> se >> >> data for --mov, thanks! >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >> >Hi Bo, >> >> > >> >> >tksurfer doesn't take a path to a file. Read the help on it - you need 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 know >> 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 spac >> e? >> >> >> >> I thought that was an easy way to go from SPM MNI to freesurfer la >> nd. >> >> >> >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathna >> me/ >> >> to/ >> >> >> spm/roi/yourfile.img/ >> >> >> >> >> >> >> >> >> >> >> >> I am wondering because when I look at the segmentation for fsaverag >> e, >> >> >> >> it seems like it is missing a lot of the gray matter, particularly >> 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 suggest >> ing >> >> >> >> >> >> (as it seemed like in this thread), to put the SPM roi into individ >> 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 Compliance >> 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 sender a >> nd >> >> pro >> >> >> perly >> >> >> >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.
