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 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. >> >> > >> >> >> >> >> >> >> >> >> >> >> >>