And what is the data you analyzed in spm? You could use the mni space mask but it won't be very accurate.
On Jun 17, 2013, at 8:44 PM, xiangbo_2010 xiangbo_2010@126.com wrote:
Hi Bruce
I use the SPM to analysis my data, and use the xjview to get a mask (have .img and .hdr files) as ROI, use the MNI space in SPM analysis. Following I want to obtain the cortical thickness from this mask in Freesurfer, and I have analyzed all my individual subjects in FreeSurfer(recon-all). thanks!
Bo
At 2013-06-18 02:35:40,"Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
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" fischl@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" fischl@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" fischl@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" fischl@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" <fischl@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" <fischl@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" <greve@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 > >> >> >> >> >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/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 > >> 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. > >> >> >> >> > > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> > >> >> > >> >> > >> >> > >> > >> > >> > >> > >> > >> > > > >