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 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 . If the e-mail was sent to
>> yo
>> >> u i
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>> r a
>> >> nd
>> >> >> pro
>> >> >> >> perly
>> >> >> >> >dispose of the e-mail.
>> >> >> >> >
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