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" fischl@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" fischl@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 f
rom
>> the mask, thanks! >> Bo >> >> >> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" fischl@nmr.mgh.harvard.edu 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 how t
o c
hoo >> se >> >> data for --mov, thanks! >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" fischl@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 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 -overl
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" <greve@nmr.mgh.harvard.
edu
> w >> rot >> >> e: >> >> >> >Hi Stephanie, I don't know which recommendation you are referri
ng
to. >> We >> >> >> >> >> >get a lot of emails, and I can't remember each one. Can you 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 fsvareg
e s
pac >> e? >> >> >> >> I thought that was an easy way to go from SPM MNI to freesur
fer
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 fs
ave
rag >> e, >> >> >> >> it seems like it is missing a lot of the gray matter, particu
lar
ly >> in >> >> >> >> the big sulci, most likely from the 'smoothing' that comes wi
th
>> >> >> >> averaging subjects together. And therefore I wonder if this
is
the >> >> >> >> >> best thing to use as an intermediate step. Are you instead s
ugg
est >> ing >> >> >> >> >> >> (as it seemed like in this thread), to put the SPM roi into i
ndi
vid >> ual >> >> >> >> >> >> subject space and then somehow project it to the surface in 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/neuroimagi
ng/
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 >> >> >> >greve@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/fl
at/
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 Compl
ian
ce >> Hel >> >> pLi >> >> >> ne at >> >> >> >http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
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. >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>