are you trying to do this for a single subject or for a group of subjects
, or group average data?
On Tue, 18 Jun 2013, xiangbo_2010 wrote:
my subject has finished the recon-all on the structural image, whether use
the command: "mri_vol2surf --src sig.img --src_type analyze --srcreg
register.dat --hemi rh --o ./sig-rh.img --out_type analyze --float2int round
--trgsubject ico --icoorder 7" to obtain the result? thanks!
Bo
At 2013-06-18 00:00:09,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>and what subject do you wan to obtain thickness measures from? You could
>use mri_vol2vol to map your mask to the individual using the MNI
>transform
>On Mon, 17 Jun 2013, xiangbo_2010 wrote:
>
>> the mask was obtained from xjview, and use the MNI space in my study,
>> thanks!
>> Bo
>>
>>
>>
>>
>>
>> At 2013-06-17 23:52:33,"Bruce Fischl" <fis...@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" <fis...@nmr.mgh.harvard.edu> wro
te:
>> >> >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 im
age
>> >> >
>> >> >
>> >> >On Mon, 17 Jun 2013, xiangbo_2010
>> >> >wrote:
>> >> >
>> >> >> I have obtained the mask from xjview (.img), I want to obtain the C
T f
>> rom
>> >> >> the mask, thanks!
>> >> >> Bo
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
wro
>> te:
>> >> >> >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 ho
w t
>> o c
>> >> hoo
>> >> >> se
>> >> >> >> data for --mov, thanks!
>> >> >> >>
>> >> >> >> Bo
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" <fis...@nmr.mgh.harvard.ed
u>
>> wro
>> >> te:
>> >> >> >> >Hi Bo,
>> >> >> >> >
>> >> >> >> >tksurfer doesn't take a path to a file. Read the help on it - y
ou
>> 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, wit
h t
>> he
>> >> >> >> >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 -ov
erl
>> ay
>> >> /pa
>> >> >> thn
>> >> >> >> ame/to/s
>> >> >> >> >> pm/roi/yourfile.img/", but do not have results for me, and do
no
>> t k
>> >> now
>> >> >> ho
>> >> >> >> w
>> >> >> >> >> to do next? thanks!
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> Bo
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> At 2013-06-06 23:04:30,"Douglas N Greve" <gr...@nmr.mgh.harva
rd.
>> edu
>> >> > w
>> >> >> rot
>> >> >> >> e:
>> >> >> >> >> >Hi Stephanie, I don't know which recommendation you are refe
rri
>> ng
>> >> to.
>> >> >> We
>> >> >> >>
>> >> >> >> >> >get a lot of emails, and I can't remember each one. Can you
rep
>> ost
>> >> 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 fsva
reg
>> e s
>> >> pac
>> >> >> e?
>> >> >> >> >> >> I thought that was an easy way to go from SPM MNI to free
sur
>> fer
>> >> la
>> >> >> nd.
>> >> >> >> >> >>
>> >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overla
y /
>> pat
>> >> hna
>> >> >> me/
>> >> >> >> to/
>> >> >> >> >> spm/roi/yourfile.img/
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> I am wondering because when I look at the segmentation for
fs
>> ave
>> >> rag
>> >> >> e,
>> >> >> >> >> >> it seems like it is missing a lot of the gray matter, part
icu
>> lar
>> >> ly
>> >> >> in
>> >> >> >> >> >> the big sulci, most likely from the 'smoothing' that comes
wi
>> th
>> >> >> >> >> >> averaging subjects together. And therefore I wonder if th
is
>> is
>> >> the
>> >> >>
>> >> >> >> >> >> best thing to use as an intermediate step. Are you instea
d s
>> ugg
>> >> est
>> >> >> ing
>> >> >> >>
>> >> >> >> >> >> (as it seemed like in this thread), to put the SPM roi int
o i
>> ndi
>> >> vid
>> >> >> ual
>> >> >> >>
>> >> >> >> >> >> subject space and then somehow project it to the surface i
n f
>> ree
>> >> 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/neuroim
agi
>> ng/
>> >> inf
>> >> >> orm
>> >> >> >> ati
>> >> >> >> >> on-investigators/faq
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> _______________________________________________
>> >> >> >> >> >> Freesurfer mailing list
>> >> >> >> >> >> Freesurfer@nmr.mgh.harvard.edu
>> >> >> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf
er
>> >> >> >> >> >
>> >> >> >> >> >--
>> >> >> >> >> >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
/fl
>> at/
>> >> 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 pers
on
>> to
>> >> who
>> >> >> m i
>> >> >> >> t i
>> >> >> >> >> s
>> >> >> >> >> >addressed. If you believe this e-mail was sent to you in err
or
>> and
>> >> th
>> >> >> e e
>> >> >> >> -ma
>> >> >> >> >> il
>> >> >> >> >> >contains patient information, please contact the Partners Co
mpl
>> ian
>> >> ce
>> >> >> Hel
>> >> >> >> pLi
>> >> >> >> >> ne at
>> >> >> >> >> >http://www.partners.org/complianceline . If the e-mail was s
ent
>> to
>> >> yo
>> >> >> u i
>> >> >> >> n e
>> >> >> >> >> rror
>> >> >> >> >> >but does not contain patient information, please contact the
se
>> nde
>> >> r a
>> >> >> nd
>> >> >> >> pro
>> >> >> >> >> perly
>> >> >> >> >> >dispose of the e-mail.
>> >> >> >> >> >
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>>
>>
>>
>>
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