p.s. you wouldn't use bert as your subject - you would specify your own 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 from the mask, thanks! Bo At 2013-06-17 22:40:43,"Bruce Fischl" fischl@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" 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 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" <greve@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 >> >> >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/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%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
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. >> >> > >> >> >> >> >> >> >> >> >> >> >> >>