Hi Bruce
I use the SPM to analysis my data, and use the xjview to get a mask (have .img and .hdr files) as ROI, use the MNI space in SPM analysis. Following I want to obtain the cortical thickness from this mask in Freesurfer, and I have analyzed all my individual subjects in FreeSurfer(recon-all). thanks! Bo At 2013-06-18 02:35:40,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >can you give a complete description of your study and what you are trying >to achieve? Have you analyzed all your individual subjects in FreeSurfer >(recon-all)? What is the mask you want to use? > >On Tue, 18 Jun 2013, xiangbo_2010 wrote: > >> I want to obtain the cortical thickness from a group of subjects, thanks! >> >> >> >> >> >> At 2013-06-18 00:13:08,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >are you trying to do this for a single subject or for a group of subjects >> >, or group average data? >> >On Tue, 18 Jun 2013, xiangbo_2010 wrote: >> > >> >> my subject has finished the recon-all on the structural image, whether us >> e >> >> the command: "mri_vol2surf --src sig.img --src_type analyze --srcreg >> >> register.dat --hemi rh --o ./sig-rh.img --out_type analyze --float2int ro >> und >> >> --trgsubject ico --icoorder 7" to obtain the result? thanks! >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-18 00:00:09,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >> >and what subject do you wan to obtain thickness measures from? You could >> >> >> >use mri_vol2vol to map your mask to the individual using the MNI >> >> >transform >> >> >On Mon, 17 Jun 2013, xiangbo_2010 wrote: >> >> > >> >> >> 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> wro >> te: >> >> >> >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 .hd >> r, >> >> >> >> whether I should convert the file (.img and .hdr) to file (.nii), a >> nd >> >> 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> >> wro >> >> te: >> >> >> >> >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 >> im >> >> age >> >> >> >> > >> >> >> >> > >> >> >> >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >> >> >> >wrote: >> >> >> >> > >> >> >> >> >> I have obtained the mask from xjview (.img), I want to obtain th >> e C >> >> T f >> >> >> rom >> >> >> >> >> the mask, thanks! >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" <fis...@nmr.mgh.harvard.ed >> u> >> >> wro >> >> >> te: >> >> >> >> >> >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 >> ho >> >> w t >> >> >> o c >> >> >> >> hoo >> >> >> >> >> se >> >> >> >> >> >> data for --mov, thanks! >> >> >> >> >> >> >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" <fis...@nmr.mgh.harvard >> .ed >> >> u> >> >> >> wro >> >> >> >> te: >> >> >> >> >> >> >Hi Bo, >> >> >> >> >> >> > >> >> >> >> >> >> >tksurfer doesn't take a path to a file. Read the help on it >> - y >> >> ou >> >> >> nee >> >> >> >> d t >> >> >> >> >> o >> >> >> >> >> >> >reconstrcut the subject with recon-all then give it the subj >> ect >> >> id >> >> >> . >> >> >> >> To >> >> >> >> >> >> >project a volumetric map onto the surface use mri_vol2surf, >> wit >> >> h t >> >> >> he >> >> >> >> >> >> >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 >> -ov >> >> erl >> >> >> ay >> >> >> >> /pa >> >> >> >> >> thn >> >> >> >> >> >> ame/to/s >> >> >> >> >> >> >> pm/roi/yourfile.img/", but do not have results for me, and >> do >> >> no >> >> >> t k >> >> >> >> now >> >> >> >> >> ho >> >> >> >> >> >> w >> >> >> >> >> >> >> to do next? thanks! >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-06 23:04:30,"Douglas N Greve" <gr...@nmr.mgh.ha >> rva >> >> rd. >> >> >> edu >> >> >> >> > w >> >> >> >> >> rot >> >> >> >> >> >> e: >> >> >> >> >> >> >> >Hi Stephanie, I don't know which recommendation you are r >> efe >> >> rri >> >> >> ng >> >> >> >> to. >> >> >> >> >> We >> >> >> >> >> >> >> >> >> >> >> >> >> >get a lot of emails, and I can't remember each one. Can y >> ou >> >> rep >> >> >> ost >> >> >> >> 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 f >> sva >> >> reg >> >> >> e s >> >> >> >> pac >> >> >> >> >> e? >> >> >> >> >> >> >> >> I thought that was an easy way to go from SPM MNI to f >> ree >> >> sur >> >> >> fer >> >> >> >> la >> >> >> >> >> nd. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -ove >> rla >> >> y / >> >> >> pat >> >> >> >> hna >> >> >> >> >> me/ >> >> >> >> >> >> to/ >> >> >> >> >> >> >> spm/roi/yourfile.img/ >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> I am wondering because when I look at the segmentation >> for >> >> fs >> >> >> ave >> >> >> >> rag >> >> >> >> >> e, >> >> >> >> >> >> >> >> it seems like it is missing a lot of the gray matter, p >> art >> >> icu >> >> >> lar >> >> >> >> ly >> >> >> >> >> in >> >> >> >> >> >> >> >> the big sulci, most likely from the 'smoothing' that co >> mes >> >> wi >> >> >> th >> >> >> >> >> >> >> >> averaging subjects together. And therefore I wonder if >> th >> >> is >> >> >> is >> >> >> >> the >> >> >> >> >> >> >> >> >> >> >> >> >> best thing to use as an intermediate step. Are you ins >> tea >> >> d s >> >> >> ugg >> >> >> >> est >> >> >> >> >> ing >> >> >> >> >> >> >> >> >> >> >> >> >> >> (as it seemed like in this thread), to put the SPM roi >> int >> >> o i >> >> >> ndi >> >> >> >> vid >> >> >> >> >> ual >> >> >> >> >> >> >> >> >> >> >> >> >> >> subject space and then somehow project it to the surfac >> e i >> >> n f >> >> >> ree >> >> >> >> 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/neur >> oim >> >> agi >> >> >> ng/ >> >> >> >> inf >> >> >> >> >> orm >> >> >> >> >> >> ati >> >> >> >> >> >> >> on-investigators/faq >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> >> >> >> >> Freesurfer mailing list >> >> >> >> >> >> >> >> Freesurfer@nmr.mgh.harvard.edu >> >> >> >> >> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees >> urf >> >> er >> >> >> >> >> >> >> > >> >> >> >> >> >> >> >-- >> >> >> >> >> >> >> >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/outgo >> ing >> >> /fl >> >> >> at/ >> >> >> >> gre >> >> >> >> >> ve/ >> >> >> >> >> >> >> > >> >> >> >> >> >> >> >_______________________________________________ >> >> >> >> >> >> >> >Freesurfer mailing list >> >> >> >> >> >> >> >Freesurfer@nmr.mgh.harvard.edu >> >> >> >> >> >> >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur >> fer >> >> >> >> >> >> >> > >> >> >> >> >> >> >> > >> >> >> >> >> >> >> >The information in this e-mail is intended only for the p >> ers >> >> on >> >> >> to >> >> >> >> who >> >> >> >> >> m i >> >> >> >> >> >> t i >> >> >> >> >> >> >> s >> >> >> >> >> >> >> >addressed. If you believe this e-mail was sent to you in >> err >> >> or >> >> >> and >> >> >> >> th >> >> >> >> >> e e >> >> >> >> >> >> -ma >> >> >> >> >> >> >> il >> >> >> >> >> >> >> >contains patient information, please contact the Partners >> Co >> >> mpl >> >> >> ian >> >> >> >> ce >> >> >> >> >> Hel >> >> >> >> >> >> pLi >> >> >> >> >> >> >> ne at >> >> >> >> >> >> >> >http://www.partners.org/complianceline . If the e-mail wa >> s s >> >> ent >> >> >> to >> >> >> >> yo >> >> >> >> >> u i >> >> >> >> >> >> n e >> >> >> >> >> >> >> rror >> >> >> >> >> >> >> >but does not contain patient information, please contact >> the >> >> se >> >> >> nde >> >> >> >> r a >> >> >> >> >> nd >> >> >> >> >> >> pro >> >> >> >> >> >> >> perly >> >> >> >> >> >> >> >dispose of the e-mail. >> >> >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
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