And what is the data you analyzed in spm? You could use the mni space mask but it won't be very accurate.
On Jun 17, 2013, at 8:44 PM, xiangbo_2010 <xiangbo_2...@126.com> wrote: > 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. 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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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