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" <fis...@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" <fis...@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" <fis...@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" <gr...@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
>> >> >> >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/outgoing/flat/
gre
>> ve/
>> >> >> >
>> >> >> >_______________________________________________
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>> >> >> >
>> >> >> >
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