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" fischl@nmr.mgh.harvard.edu wrote:

...

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 image

On Mon, 17 Jun 2013, xiangbo_2010  wrote:

...

I have obtained the mask from xjview (.img), I want to obtain the CT from  the mask, thanks!  Bo            At 2013-06-17 22:40:43,"Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:  >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 how to c

hoo

...

...

se  >> data for  --mov, thanks!  >>   >> Bo  >>   >>   >>   >>   >> At 2013-06-17 20:34:39,"Bruce Fischl" fischl@nmr.mgh.harvard.edu wro

te:

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...

>> >Hi Bo,  >> >  >> >tksurfer doesn't take a path to a file. Read the help on it - you nee

d t

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...

o   >> >reconstrcut the subject with recon-all then give it the subject id.

To

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...

>> >project a volumetric map onto the surface use mri_vol2surf, with the   >> >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 -overlay

/pa

...

...

thn  >> ame/to/s   >> >> pm/roi/yourfile.img/", but do not have results for me, and do not k

now

...

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ho  >> w  >> >> to do next? thanks!  >> >>   >> >>   >> >> Bo  >> >>   >> >>   >> >>   >> >>   >> >>   >> >> At 2013-06-06 23:04:30,"Douglas N Greve" <greve@nmr.mgh.harvard.edu

w

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rot  >> e:  >> >> >Hi Stephanie, I don't know which recommendation you are referring

to.

...

...

We  >>    >> >> >get a lot of emails, and I can't remember each one. Can you repost

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 fsvarege s

pac

...

...

e?   >> >> >>  I thought that was an easy way to go from SPM MNI to freesurfer

la

...

...

nd.  >> >> >>  >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pat

hna

...

...

me/  >> to/  >> >> spm/roi/yourfile.img/  >> >> >>  >> >> >>  >> >> >> I am wondering because when I look at the segmentation for fsave

rag

...

...

e,   >> >> >> it seems like it is missing a lot of the gray matter, particular

ly

...

...

in   >> >> >> the big sulci, most likely from the 'smoothing' that comes with   >> >> >> averaging subjects together.  And therefore I wonder if this is

the

...

...

>> >> >> best thing to use as an intermediate step.  Are you instead sugg

est

...

...

ing  >>    >> >> >> (as it seemed like in this thread), to put the SPM roi into indi

vid

...

...

ual  >>    >> >> >> subject space and then somehow project it to the surface in free

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/neuroimaging/

inf

...

...

orm  >> ati  >> >> on-investigators/faq  >> >> >>  >> >> >>  >> >> >>  >> >> >>  >> >> >>  >> >> >>  >> >> >>  >> >> >>  >> >> >>  >> >> >> _______________________________________________  >> >> >> Freesurfer mailing list  >> >> >> Freesurfer@nmr.mgh.harvard.edu  >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  >> >> >  >> >> >--   >> >> >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/outgoing/flat/

gre

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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 person to

who

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...

m i  >> t i  >> >> s  >> >> >addressed. If you believe this e-mail was sent to you in error and

th

...

...

e e  >> -ma  >> >> il  >> >> >contains patient information, please contact the Partners Complian

ce

...

...

Hel  >> pLi  >> >> ne at  >> >> >http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...

yo

...

...

u i  >> n e  >> >> rror  >> >> >but does not contain patient information, please contact the sende

r a

...

...

nd   >> pro  >> >> perly  >> >> >dispose of the e-mail.  >> >> >  >> >>   >> >>   >> >>   >> >>  >>   >>   >>   >>

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 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" fischl@nmr.mgh.harvard.edu wrote:  >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 image  >  >  >On Mon, 17 Jun 2013, xiangbo_2010   >wrote:  >  >> I have obtained the mask from xjview (.img), I want to obtain the CT f

rom

...

...

>> the mask, thanks!  >> Bo  >>   >>   >>   >>   >>   >> At 2013-06-17 22:40:43,"Bruce Fischl" fischl@nmr.mgh.harvard.edu wro

te:

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...

>> >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 how t

o c

...

...

hoo  >> se  >> >> data for  --mov, thanks!  >> >>   >> >> Bo  >> >>   >> >>   >> >>   >> >>   >> >> At 2013-06-17 20:34:39,"Bruce Fischl" fischl@nmr.mgh.harvard.edu

wro

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...

te:  >> >> >Hi Bo,  >> >> >  >> >> >tksurfer doesn't take a path to a file. Read the help on it - you

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, with 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 -overl

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.harvard.

edu

...

...

> w  >> rot  >> >> e:  >> >> >> >Hi Stephanie, I don't know which recommendation you are referri

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 fsvareg

e s

...

...

pac  >> e?   >> >> >> >>  I thought that was an easy way to go from SPM MNI to freesur

fer

...

...

la  >> nd.  >> >> >> >>  >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /

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, particu

lar

...

...

ly   >> in   >> >> >> >> the big sulci, most likely from the 'smoothing' that comes wi

th

...

...

>> >> >> >> averaging subjects together.  And therefore I wonder if this

is

...

...

the  >>    >> >> >> >> best thing to use as an intermediate step.  Are you instead s

ugg

...

...

est  >> ing  >> >>    >> >> >> >> (as it seemed like in this thread), to put the SPM roi into i

ndi

...

...

vid  >> ual  >> >>    >> >> >> >> subject space and then somehow project it to the surface in 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/neuroimagi

ng/

...

...

inf  >> orm  >> >> ati  >> >> >> on-investigators/faq  >> >> >> >>  >> >> >> >>  >> >> >> >>  >> >> >> >>  >> >> >> >>  >> >> >> >>  >> >> >> >>  >> >> >> >>  >> >> >> >>  >> >> >> >> _______________________________________________  >> >> >> >> Freesurfer mailing list  >> >> >> >> Freesurfer@nmr.mgh.harvard.edu  >> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  >> >> >> >  >> >> >> >--   >> >> >> >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/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 person

to

...

...

who  >> m i  >> >> t i  >> >> >> s  >> >> >> >addressed. If you believe this e-mail was sent to you in error

and

...

...

th  >> e e  >> >> -ma  >> >> >> il  >> >> >> >contains patient information, please contact the Partners Compl

ian

...

...

ce   >> Hel  >> >> pLi  >> >> >> ne at  >> >> >> >http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...

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.  >> >> >> >  >> >> >>   >> >> >>   >> >> >>   >> >> >>  >> >>   >> >>   >> >>   >> >>  >>   >>   >>   >>

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" 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 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" 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 the C

T f

...

...

rom  >> >> the mask, thanks!  >> >> Bo  >> >>   >> >>   >> >>   >> >>   >> >>   >> >> At 2013-06-17 22:40:43,"Bruce Fischl" fischl@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" <fischl@nmr.mgh.harvard.ed

u>

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...

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

...

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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

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ay   >> /pa  >> >> thn  >> >> >> ame/to/s   >> >> >> >> pm/roi/yourfile.img/", but do not have results for me, and do

no

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t k  >> now  >> >>  ho  >> >> >> w  >> >> >> >> to do next? thanks!  >> >> >> >>   >> >> >> >>   >> >> >> >> Bo  >> >> >> >>   >> >> >> >>   >> >> >> >>   >> >> >> >>   >> >> >> >>   >> >> >> >> At 2013-06-06 23:04:30,"Douglas N Greve" <greve@nmr.mgh.harva

rd.

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edu  >> > w  >> >> rot  >> >> >> e:  >> >> >> >> >Hi Stephanie, I don't know which recommendation you are refe

rri

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ng   >> to.  >> >>  We  >> >> >>    >> >> >> >> >get a lot of emails, and I can't remember each one. Can you

rep

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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

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e s  >> pac  >> >> e?   >> >> >> >> >>  I thought that was an easy way to go from SPM MNI to free

sur

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fer  >>  la  >> >> nd.  >> >> >> >> >>  >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overla

y /

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pat  >> hna  >> >> me/  >> >> >> to/  >> >> >> >> spm/roi/yourfile.img/  >> >> >> >> >>  >> >> >> >> >>  >> >> >> >> >> I am wondering because when I look at the segmentation for

fs

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ave  >> rag  >> >> e,   >> >> >> >> >> it seems like it is missing a lot of the gray matter, part

icu

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lar  >> ly   >> >> in   >> >> >> >> >> the big sulci, most likely from the 'smoothing' that comes

wi

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th   >> >> >> >> >> averaging subjects together.  And therefore I wonder if th

is

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is   >> the  >> >>    >> >> >> >> >> best thing to use as an intermediate step.  Are you instea

d s

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ugg  >> est  >> >> ing  >> >> >>    >> >> >> >> >> (as it seemed like in this thread), to put the SPM roi int

o i

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ndi  >> vid  >> >> ual  >> >> >>    >> >> >> >> >> subject space and then somehow project it to the surface i

n f

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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

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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

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>> >> >> >> >  >> >> >> >> >--   >> >> >> >> >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/outgoing

/fl

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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

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to   >> who  >> >> m i  >> >> >> t i  >> >> >> >> s  >> >> >> >> >addressed. If you believe this e-mail was sent to you in err

or

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and  >>  th  >> >> e e  >> >> >> -ma  >> >> >> >> il  >> >> >> >> >contains patient information, please contact the Partners Co

mpl

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ian  >> ce   >> >> Hel  >> >> >> pLi  >> >> >> >> ne at  >> >> >> >> >http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...

ent

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to  >>  yo  >> >> u i  >> >> >> n e  >> >> >> >> rror  >> >> >> >> >but does not contain patient information, please contact the

se

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nde  >> r a  >> >> nd   >> >> >> pro  >> >> >> >> perly  >> >> >> >> >dispose of the e-mail.  >> >> >> >> >  >> >> >> >>   >> >> >> >>   >> >> >> >>   >> >> >> >>  >> >> >>   >> >> >>   >> >> >>   >> >> >>  >> >>   >> >>   >> >>   >> >>  >>   >>   >>   >>   >>   >>

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:

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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:

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my subject has finished the recon-all on the structural image, whether us

e

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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

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--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

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>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:

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>> >sorry, the formatting of your emails is lost in my reader and you may

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>> >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

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>> >> obtained the mask from SPM which include the file with .img and .hd

r,

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>> >> whether I should convert the file (.img and .hdr) to file (.nii), a

nd

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use  >> >> the command:  "bbregister --s bert --mov func.nii --init-spm --reg  >> >> register.dat tkregister2 --mov func.nii --reg register.dat --surf "

to

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>> >> obtain the result? thanks!  >> >>   >> >> Bo  >> >>   >> >>   >> >>   >> >>   >> >>   >> >> At 2013-06-17 23:07:19,"Bruce Fischl" fischl@nmr.mgh.harvard.edu

wro

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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

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age  >> >> >  >> >> >  >> >> >On Mon, 17 Jun 2013, xiangbo_2010   >> >> >wrote:  >> >> >  >> >> >> I have obtained the mask from xjview (.img), I want to obtain th

e C

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T f  >> rom  >> >> >> the mask, thanks!  >> >> >> Bo  >> >> >>   >> >> >>   >> >> >>   >> >> >>   >> >> >>   >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" <fischl@nmr.mgh.harvard.ed

u>

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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

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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

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u>   >> wro  >> >> te:  >> >> >> >> >Hi Bo,  >> >> >> >> >  >> >> >> >> >tksurfer doesn't take a path to a file. Read the help on it

- y

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ou   >> nee  >> >> d t  >> >> >> o   >> >> >> >> >reconstrcut the subject with recon-all then give it the subj

ect

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id  >> .    >> >> To   >> >> >> >> >project a volumetric map onto the surface use mri_vol2surf,

wit

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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

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erl  >> ay   >> >> /pa  >> >> >> thn  >> >> >> >> ame/to/s   >> >> >> >> >> pm/roi/yourfile.img/", but do not have results for me, and

do

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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

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rd.  >> edu  >> >> > w  >> >> >> rot  >> >> >> >> e:  >> >> >> >> >> >Hi Stephanie, I don't know which recommendation you are r

efe

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rri  >> ng   >> >> to.  >> >> >>  We  >> >> >> >>    >> >> >> >> >> >get a lot of emails, and I can't remember each one. Can y

ou

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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

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reg  >> e s  >> >> pac  >> >> >> e?   >> >> >> >> >> >>  I thought that was an easy way to go from SPM MNI to f

ree

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sur  >> fer  >> >>  la  >> >> >> nd.  >> >> >> >> >> >>  >> >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -ove

rla

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y /  >> pat  >> >> hna  >> >> >> me/  >> >> >> >> to/  >> >> >> >> >> spm/roi/yourfile.img/  >> >> >> >> >> >>  >> >> >> >> >> >>  >> >> >> >> >> >> I am wondering because when I look at the segmentation

for

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fs  >> ave  >> >> rag  >> >> >> e,   >> >> >> >> >> >> it seems like it is missing a lot of the gray matter, p

art

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icu  >> lar  >> >> ly   >> >> >> in   >> >> >> >> >> >> the big sulci, most likely from the 'smoothing' that co

mes

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wi  >> th   >> >> >> >> >> >> averaging subjects together.  And therefore I wonder if

th

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is   >> is   >> >> the  >> >> >>    >> >> >> >> >> >> best thing to use as an intermediate step.  Are you ins

tea

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d s  >> ugg  >> >> est  >> >> >> ing  >> >> >> >>    >> >> >> >> >> >> (as it seemed like in this thread), to put the SPM roi

int

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o i  >> ndi  >> >> vid  >> >> >> ual  >> >> >> >>    >> >> >> >> >> >> subject space and then somehow project it to the surfac

e i

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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

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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

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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

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/fl  >> at/  >> >> gre  >> >> >> ve/  >> >> >> >> >> >  >> >> >> >> >> >_______________________________________________  >> >> >> >> >> >Freesurfer mailing list  >> >> >> >> >> >Freesurfer@nmr.mgh.harvard.edu  >> >> >> >> >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

fer

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>> >> >> >> >> >  >> >> >> >> >> >  >> >> >> >> >> >The information in this e-mail is intended only for the p

ers

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on   >> to   >> >> who  >> >> >> m i  >> >> >> >> t i  >> >> >> >> >> s  >> >> >> >> >> >addressed. If you believe this e-mail was sent to you in

err

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or   >> and  >> >>  th  >> >> >> e e  >> >> >> >> -ma  >> >> >> >> >> il  >> >> >> >> >> >contains patient information, please contact the Partners

Co

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mpl  >> ian  >> >> ce   >> >> >> Hel  >> >> >> >> pLi  >> >> >> >> >> ne at  >> >> >> >> >> >http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...

s s

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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.  >> >> >> >> >> >  >> >> >> >> >>   >> >> >> >> >>   >> >> >> >> >>   >> >> >> >> >>  >> >> >> >>   >> >> >> >>   >> >> >> >>   >> >> >> >>  >> >> >>   >> >> >>   >> >> >>   >> >> >>  >> >>   >> >>   >> >>   >> >>   >> >>   >> >>  >>   >>   >>   >>

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. > >> >> >> >> > > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> > >> >> > >> >> > >> >> > >> > >> > >> > >> > >> > >> > > > >

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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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
<mailto: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  <mailto: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  <mailto: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  <mailto: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  <mailto: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  <mailto: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  <mailto: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  <mailto: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  <mailto: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  <mailto: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  <mailto: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  <mailto: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.
>> >> >> >> >> >> >> >
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >>
>> >>
>> >>
>> >>
>>
>>
>>
>>

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