can you give a complete description of your study and what you are trying
to achieve? Have you analyzed all your individual subjects in FreeSurfer
(recon-all)? What is the mask you want to use?
On Tue, 18 Jun 2013, xiangbo_2010 wrote:
I want to obtain the cortical thickness from a group of subjects, thanks!
At 2013-06-18 00:13:08,"Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>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 us
e
>> the command: "mri_vol2surf --src sig.img --src_type analyze --srcreg
>> register.dat --hemi rh --o ./sig-rh.img --out_type analyze --float2int ro
und
>> --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> wro
te:
>> >> >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 .hd
r,
>> >> >> whether I should convert the file (.img and .hdr) to file (.nii), a
nd
>> 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 th
e C
>> T f
>> >> rom
>> >> >> >> the mask, thanks!
>> >> >> >> Bo
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" <fis...@nmr.mgh.harvard.ed
u>
>> 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 subj
ect
>> 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.ha
rva
>> rd.
>> >> edu
>> >> >> > w
>> >> >> >> rot
>> >> >> >> >> e:
>> >> >> >> >> >> >Hi Stephanie, I don't know which recommendation you are r
efe
>> rri
>> >> ng
>> >> >> to.
>> >> >> >> We
>> >> >> >> >>
>> >> >> >> >> >> >get a lot of emails, and I can't remember each one. Can y
ou
>> 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 f
sva
>> reg
>> >> e s
>> >> >> pac
>> >> >> >> e?
>> >> >> >> >> >> >> I thought that was an easy way to go from SPM MNI to f
ree
>> sur
>> >> fer
>> >> >> la
>> >> >> >> nd.
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -ove
rla
>> 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, p
art
>> icu
>> >> lar
>> >> >> ly
>> >> >> >> in
>> >> >> >> >> >> >> the big sulci, most likely from the 'smoothing' that co
mes
>> wi
>> >> th
>> >> >> >> >> >> >> averaging subjects together. And therefore I wonder if
th
>> is
>> >> is
>> >> >> the
>> >> >> >>
>> >> >> >> >> >> >> best thing to use as an intermediate step. Are you ins
tea
>> 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 surfac
e 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/neur
oim
>> agi
>> >> ng/
>> >> >> inf
>> >> >> >> orm
>> >> >> >> >> ati
>> >> >> >> >> >> on-investigators/faq
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >> _______________________________________________
>> >> >> >> >> >> >> Freesurfer mailing list
>> >> >> >> >> >> >> Freesurfer@nmr.mgh.harvard.edu
>> >> >> >> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees
urf
>> 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/outgo
ing
>> /fl
>> >> at/
>> >> >> gre
>> >> >> >> ve/
>> >> >> >> >> >> >
>> >> >> >> >> >> >_______________________________________________
>> >> >> >> >> >> >Freesurfer mailing list
>> >> >> >> >> >> >Freesurfer@nmr.mgh.harvard.edu
>> >> >> >> >> >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur
fer
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> >The information in this e-mail is intended only for the p
ers
>> 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 wa
s s
>> ent
>> >> to
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>> >> >> >> >> n e
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the
>> se
>> >> nde
>> >> >> r a
>> >> >> >> nd
>> >> >> >> >> pro
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>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >>
>> >>
>> >>
>> >>
>>
>>
>>
>>
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