I 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 choo
se
data for --mov, thanks!
Bo
At 2013-06-17 20:34:39,"Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Bo,
tksurfer doesn't take a path to a file. Read the help on it - you need 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 know
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 spac
e?
>> I thought that was an easy way to go from SPM MNI to freesurfer la
nd.
>> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathna
me/
to/
spm/roi/yourfile.img/ >> >> >> I am wondering because when I look at the segmentation for fsaverag
e,
>> it seems like it is missing a lot of the gray matter, particularly
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 suggest
ing
>> (as it seemed like in this thread), to put the SPM roi into individ
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/
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