From thomas.thesen@med.nyu.edu Thu Jan 6 17:48:52 2011 From: "Thesen, Thomas" To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] variance or stdev from average Date: Thu, 06 Jan 2011 17:48:48 -0500 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============0298402085562883154==" --===============0298402085562883154== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi, I am using mris_average_curvature to create an average thickness map across s= ubjects (registered to fsaverage). The command line I am running is: mris_average_curvature lh.thickness lh sphere.reg subj01 subj02 .... subj20 = outputfile This produces the average, but my question is if there a way to also create a= measure of variability at the vertex level from that group, e.g. the associa= ted variance or standard deviation? Thanks, Thomas ------------------------------------------------------------
This email message, including any attachments, is for the sole use of the int= ended recipient(s) and may contain information that is proprietary, confident= ial, and exempt from disclosure under applicable law. Any unauthorized review= , use, disclosure, or distribution is prohibited. If you have received this e= mail in error please notify the sender by return email and delete the origina= l message. Please note, the recipient should check this email and any attachm= ents for the presence of viruses. The organization accepts no liability for a= ny damage caused by any virus transmitted by this email.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D




--===============0298402085562883154==
Content-Type: text/html
Content-Transfer-Encoding: base64
Content-Disposition: attachment; filename="attachment.html"
MIME-Version: 1.0

PGh0bWwgeG1sbnM6dj0idXJuOnNjaGVtYXMtbWljcm9zb2Z0LWNvbTp2bWwiIHhtbG5zOm89InVy
bjpzY2hlbWFzLW1pY3Jvc29mdC1jb206b2ZmaWNlOm9mZmljZSIgeG1sbnM6dz0idXJuOnNjaGVt
YXMtbWljcm9zb2Z0LWNvbTpvZmZpY2U6d29yZCIgeG1sbnM6bT0iaHR0cDovL3NjaGVtYXMubWlj
cm9zb2Z0LmNvbS9vZmZpY2UvMjAwNC8xMi9vbW1sIiB4bWxucz0iaHR0cDovL3d3dy53My5vcmcv
VFIvUkVDLWh0bWw0MCI+PGhlYWQ+PE1FVEEgSFRUUC1FUVVJVj0iQ29udGVudC1UeXBlIiBDT05U
RU5UPSJ0ZXh0L2h0bWw7IGNoYXJzZXQ9dXMtYXNjaWkiPjxtZXRhIG5hbWU9R2VuZXJhdG9yIGNv
bnRlbnQ9Ik1pY3Jvc29mdCBXb3JkIDEyIChmaWx0ZXJlZCBtZWRpdW0pIj48c3R5bGU+PCEtLQov
KiBGb250IERlZmluaXRpb25zICovCkBmb250LWZhY2UKCXtmb250LWZhbWlseTpDYWxpYnJpOwoJ
cGFub3NlLTE6MiAxNSA1IDIgMiAyIDQgMyAyIDQ7fQovKiBTdHlsZSBEZWZpbml0aW9ucyAqLwpw
Lk1zb05vcm1hbCwgbGkuTXNvTm9ybWFsLCBkaXYuTXNvTm9ybWFsCgl7bWFyZ2luOjBpbjsKCW1h
cmdpbi1ib3R0b206LjAwMDFwdDsKCWZvbnQtc2l6ZToxMS4wcHQ7Cglmb250LWZhbWlseToiQ2Fs
aWJyaSIsInNhbnMtc2VyaWYiO30KYTpsaW5rLCBzcGFuLk1zb0h5cGVybGluawoJe21zby1zdHls
ZS1wcmlvcml0eTo5OTsKCWNvbG9yOmJsdWU7Cgl0ZXh0LWRlY29yYXRpb246dW5kZXJsaW5lO30K
YTp2aXNpdGVkLCBzcGFuLk1zb0h5cGVybGlua0ZvbGxvd2VkCgl7bXNvLXN0eWxlLXByaW9yaXR5
Ojk5OwoJY29sb3I6cHVycGxlOwoJdGV4dC1kZWNvcmF0aW9uOnVuZGVybGluZTt9CnNwYW4uRW1h
aWxTdHlsZTE3Cgl7bXNvLXN0eWxlLXR5cGU6cGVyc29uYWwtY29tcG9zZTsKCWZvbnQtZmFtaWx5
OiJDYWxpYnJpIiwic2Fucy1zZXJpZiI7Cgljb2xvcjp3aW5kb3d0ZXh0O30KLk1zb0NocERlZmF1
bHQKCXttc28tc3R5bGUtdHlwZTpleHBvcnQtb25seTt9CkBwYWdlIFdvcmRTZWN0aW9uMQoJe3Np
emU6OC41aW4gMTEuMGluOwoJbWFyZ2luOjEuMGluIDEuMGluIDEuMGluIDEuMGluO30KZGl2Lldv
cmRTZWN0aW9uMQoJe3BhZ2U6V29yZFNlY3Rpb24xO30KLS0+PC9zdHlsZT48IS0tW2lmIGd0ZSBt
c28gOV0+PHhtbD4KPG86c2hhcGVkZWZhdWx0cyB2OmV4dD0iZWRpdCIgc3BpZG1heD0iMTAyNiIg
Lz4KPC94bWw+PCFbZW5kaWZdLS0+PCEtLVtpZiBndGUgbXNvIDldPjx4bWw+CjxvOnNoYXBlbGF5
b3V0IHY6ZXh0PSJlZGl0Ij4KPG86aWRtYXAgdjpleHQ9ImVkaXQiIGRhdGE9IjEiIC8+Cjwvbzpz
aGFwZWxheW91dD48L3htbD48IVtlbmRpZl0tLT48L2hlYWQ+PGJvZHkgbGFuZz1FTi1VUyBsaW5r
PWJsdWUgdmxpbms9cHVycGxlPjxkaXYgY2xhc3M9V29yZFNlY3Rpb24xPjxwIGNsYXNzPU1zb05v
cm1hbD5IaSw8bzpwPjwvbzpwPjwvcD48cCBjbGFzcz1Nc29Ob3JtYWw+PG86cD4mbmJzcDs8L286
cD48L3A+PHAgY2xhc3M9TXNvTm9ybWFsPkkgYW0gdXNpbmcgbXJpc19hdmVyYWdlX2N1cnZhdHVy
ZSB0byBjcmVhdGUgYW4gYXZlcmFnZSB0aGlja25lc3MgbWFwIGFjcm9zcyBzdWJqZWN0cyAocmVn
aXN0ZXJlZCB0byBmc2F2ZXJhZ2UpLiA8bzpwPjwvbzpwPjwvcD48cCBjbGFzcz1Nc29Ob3JtYWw+
PG86cD4mbmJzcDs8L286cD48L3A+PHAgY2xhc3M9TXNvTm9ybWFsPlRoZSBjb21tYW5kIGxpbmUg
SSBhbSBydW5uaW5nIGlzOjxvOnA+PC9vOnA+PC9wPjxwIGNsYXNzPU1zb05vcm1hbD48bzpwPiZu
YnNwOzwvbzpwPjwvcD48cCBjbGFzcz1Nc29Ob3JtYWw+bXJpc19hdmVyYWdlX2N1cnZhdHVyZSZu
YnNwOyBsaC50aGlja25lc3MgbGggc3BoZXJlLnJlZyBzdWJqMDEgc3ViajAyICYjODIzMDsuIHN1
YmoyMCBvdXRwdXRmaWxlPG86cD48L286cD48L3A+PHAgY2xhc3M9TXNvTm9ybWFsPjxvOnA+Jm5i
c3A7PC9vOnA+PC9wPjxwIGNsYXNzPU1zb05vcm1hbD5UaGlzIHByb2R1Y2VzIHRoZSBhdmVyYWdl
LCBidXQgbXkgcXVlc3Rpb24gaXMgaWYgdGhlcmUgYSB3YXkgdG8gYWxzbyBjcmVhdGUgYSBtZWFz
dXJlIG9mIHZhcmlhYmlsaXR5IGF0IHRoZSB2ZXJ0ZXggbGV2ZWwgZnJvbSB0aGF0IGdyb3VwLCBl
LmcuIHRoZSBhc3NvY2lhdGVkIHZhcmlhbmNlIG9yIHN0YW5kYXJkIGRldmlhdGlvbj88bzpwPjwv
bzpwPjwvcD48cCBjbGFzcz1Nc29Ob3JtYWw+PG86cD4mbmJzcDs8L286cD48L3A+PHAgY2xhc3M9
TXNvTm9ybWFsPlRoYW5rcyw8bzpwPjwvbzpwPjwvcD48cCBjbGFzcz1Nc29Ob3JtYWw+VGhvbWFz
PG86cD48L286cD48L3A+PHAgY2xhc3M9TXNvTm9ybWFsPjxvOnA+Jm5ic3A7PC9vOnA+PC9wPjwv
ZGl2PjxwcmU+PC9QUkU+CjxodG1sPgo8Ym9keT4KLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t
LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tPGJyIC8+ClRoaXMgZW1haWwgbWVzc2Fn
ZSwgaW5jbHVkaW5nIGFueSBhdHRhY2htZW50cywgaXMgZm9yIHRoZSBzb2xlIHVzZSBvZiB0aGUg
aW50ZW5kZWQgcmVjaXBpZW50KHMpIGFuZCBtYXkgY29udGFpbiBpbmZvcm1hdGlvbiB0aGF0IGlz
IHByb3ByaWV0YXJ5LCBjb25maWRlbnRpYWwsIGFuZCBleGVtcHQgZnJvbSBkaXNjbG9zdXJlIHVu
ZGVyIGFwcGxpY2FibGUgbGF3LiBBbnkgdW5hdXRob3JpemVkIHJldmlldywgdXNlLCBkaXNjbG9z
dXJlLCBvciBkaXN0cmlidXRpb24gaXMgcHJvaGliaXRlZC4gSWYgeW91IGhhdmUgcmVjZWl2ZWQg
dGhpcyBlbWFpbCBpbiBlcnJvciBwbGVhc2Ugbm90aWZ5IHRoZSBzZW5kZXIgYnkgcmV0dXJuIGVt
YWlsIGFuZCBkZWxldGUgdGhlIG9yaWdpbmFsIG1lc3NhZ2UuIFBsZWFzZSBub3RlLCB0aGUgcmVj
aXBpZW50IHNob3VsZCBjaGVjayB0aGlzIGVtYWlsIGFuZCBhbnkgYXR0YWNobWVudHMgZm9yIHRo
ZSBwcmVzZW5jZSBvZiB2aXJ1c2VzLiBUaGUgb3JnYW5pemF0aW9uIGFjY2VwdHMgbm8gbGlhYmls
aXR5IGZvciBhbnkgZGFtYWdlIGNhdXNlZCBieSBhbnkgdmlydXMgdHJhbnNtaXR0ZWQgYnkgdGhp
cyBlbWFpbC48YnIgLz4KPT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09CjwvYm9keT4K
PC9odG1sPgo8UFJFPgo8L3ByZT48L2JvZHk+PC9odG1sPg==

--===============0298402085562883154==--


From fischl@nmr.mgh.harvard.edu Fri Jan  7 09:12:04 2011
From: Bruce Fischl 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] variance or stdev from average
Date: Fri, 07 Jan 2011 09:12:02 -0500
Message-ID: 
In-Reply-To:
 
MIME-Version: 1.0
Content-Type: multipart/mixed; boundary="===============5505132817219365276=="

--===============5505132817219365276==
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: quoted-printable

Hi Thomas,

you can specify -s  to generate means and variances, but I'm=20
pretty sure Doug has something more up-to-date to do this.

cheers
Bruce
On Thu, 6 Jan=20
2011, Thesen, Thomas wrote:

> Hi,
>
> I am using mris_average_curvature to create an average thickness map across=
 subjects (registered to fsaverage).
>
> The command line I am running is:
>
> mris_average_curvature  lh.thickness lh sphere.reg subj01 subj02 .... subj2=
0 outputfile
>
> This produces the average, but my question is if there a way to also create=
 a measure of variability at the vertex level from that group, e.g. the assoc=
iated variance or standard deviation?
>
> Thanks,
> Thomas
>
>

> > > ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the i= ntended recipient(s) and may contain information that is proprietary, confide= ntial, and exempt from disclosure under applicable law. Any unauthorized revi= ew, use, disclosure, or distribution is prohibited. If you have received this= email in error please notify the sender by return email and delete the origi= nal message. Please note, the recipient should check this email and any attac= hments for the presence of viruses. The organization accepts no liability for= any damage caused by any virus transmitted by this email.
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D > > >

>

--===============5505132817219365276==--


From greve@nmr.mgh.harvard.edu Fri Jan  7 09:53:34 2011
From: Douglas N Greve 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] variance or stdev from average
Date: Fri, 07 Jan 2011 09:53:29 -0500
Message-ID: <4D2728E9.6090400@nmr.mgh.harvard.edu>
In-Reply-To: 
MIME-Version: 1.0
Content-Type: multipart/mixed; boundary="===============2950116651734479650=="

--===============2950116651734479650==
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: quoted-printable

Try using mris_preproc with "--meas curv". Create a list of your=20
subjects in a text file which you then pass with the --f flag. The=20
output will be all the curvs from your subjects stacked together. You=20
can then use mri_concat with the --mean option to get the mean, or the=20
--std to get the standard dev.

doug



Bruce Fischl wrote:
> Hi Thomas,
>
> you can specify -s  to generate means and variances, but I'm=20
> pretty sure Doug has something more up-to-date to do this.
>
> cheers
> Bruce
> On Thu, 6 Jan=20
> 2011, Thesen, Thomas wrote:
>
>  =20
>> Hi,
>>
>> I am using mris_average_curvature to create an average thickness map acros=
s subjects (registered to fsaverage).
>>
>> The command line I am running is:
>>
>> mris_average_curvature  lh.thickness lh sphere.reg subj01 subj02 .... subj=
20 outputfile
>>
>> This produces the average, but my question is if there a way to also creat=
e a measure of variability at the vertex level from that group, e.g. the asso=
ciated variance or standard deviation?
>>
>> Thanks,
>> Thomas
>>
>>

>> >> >> ------------------------------------------------------------
>> This email message, including any attachments, is for the sole use of the = intended recipient(s) and may contain information that is proprietary, confid= ential, and exempt from disclosure under applicable law. Any unauthorized rev= iew, use, disclosure, or distribution is prohibited. If you have received thi= s email in error please notify the sender by return email and delete the orig= inal message. Please note, the recipient should check this email and any atta= chments for the presence of viruses. The organization accepts no liability fo= r any damage caused by any virus transmitted by this email.
>> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D >> >> >>

>>
>>    =20
> _______________________________________________
> Freesurfer mailing list
> Freesurfer(a)nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>  =20

--=20
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve(a)nmr.mgh.harvard.edu
Phone Number: 617-724-2358=20
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html


--===============2950116651734479650==--