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%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
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. >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>