Dear Doug
According the site:"https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2010-August/015294.htm...", I used the command: "mri_vol2surf --mov my data.nii.gz --reg ${FREESURFER_HOME}/average/mni152.register.dat --hemi rh --o ./rh.test.vol2surf.mgh --trgsubject fsaverage --surf inflated_pre --projfrac 0 --interp nearest" to obtain the rh.test.vol2surf.mgh, and to open it, drawing the ROI to a label, following to get every subject data. whether the above analysis is correct? thanks!
Bo
At 2013-06-18 15:00:57,"Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Bo, you should run the MNI152 template through recon-all, then map your mask to the surface, create a label, then map the label to each individual subject with mri_label2label doug
On 6/17/13 11:48 PM, xiangbo_2010 wrote:
Hi doug,
I have finished the recon-all with -qcache, should I use MNI152 template to replace -acache? thanks!
Bo
At 2013-06-18 14:28:17,"Douglas Greve" greve@nmr.mgh.harvard.edu wrote: Hi Bo, you should run the MNI152 template through recon-all, then map your mask to the surface, create a label, then map the label to each individual subject with mri_label2label doug
On 6/17/13 7:24 PM, xiangbo_2010@126.com wrote:
I analysis the volume of grey matter, and MNI152 as the mask of whole brain. Thanks!
Bo
发送自我的HTC One SU
----- Reply message ----- 发件人： "Bruce Fischl" fischl@nmr.mgh.harvard.edu 收件人： "xiangbo_2010" xiangbo_2010@126.com 抄送： "freesurfer" freesurfer@nmr.mgh.harvard.edu 主题： [Freesurfer] SPM ROI to Cortical Thickness 日期： 周二, 6 月 18 日, 2013 年 09:51
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. >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer