Thanks. I had one more question now that I'm to mri_glmfit. Based on an error message I'm getting, it seems something about my design matrix isn't set up right. I'm inputting a text file for x in which each row looks like:

1 0 0 1 0 42.35

with the first three numbers being my class variable of interest, the next two gender, and the last age. It tells me the "matrix is ill-conditioned or badly scaled, condno = 1e+08," and then prints out the matrix and aborts. Do you know what I need to do differently for this to work? Thanks,

-Aaron-

-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, February 14, 2007 11:49 AM To: Goldman, Aaron (NIH/NIMH) [C] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] smoothing question

something like:

mri_surf2surf --s subject --hemi lh --sval input --tval output --fwhm 5

doug

Goldman, Aaron (NIH/NIMH) [C] wrote:

Hi, I'm attempting to do thickness analysis based on the guide at:

http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf

For the smoothing part using mri_surf2surf (page 14), I was wondering what a typical command line should look like.

Thanks,

-Aaron-

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Darling Douglas,

Quick question, regarding: --sim nulltype nsim thresh csdbasename : simulation perm, mc- full, mc-z

in "perm" - is this cluster-based or voxel-based? what exactly does the second input argument mean? what units are the output in?

also, same questions wrt mc-z ?

And what's the difference between the two methods? Sorry for the unbridled ignorance at this end....

Cheers Monsieur

------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---

Can you send the fsgd and the design matrix?

Goldman, Aaron (NIH/NIMH) [C] wrote:

Running that, the highest off-diagonal value was about 0.095. Is that enough that it should be a problem? I also tried running mri_glmfit with a fsgd file, and it claimed it was "not formatted properly." Other than the fact that I have two class variables, my file looks identical to the example on the wiki, so I'm wondering if that was supposed to be encoded in some way other than how I did it. In that file, my lines look like:

Group Descriptor File

Title Title

Tessellation surface

Class NC

(other classes...)

Variables Age

Input Subject01 NC Male 42.35

(other subjects)

Is this how it's supposed to be?

Thanks,

-Aaron-

---

From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, February 15, 2007 12:37 PM To: Goldman, Aaron (NIH/NIMH) [C] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] smoothing question

It sounds like there's something wrong with your design matrix. Try loading it into matlab and looking X'*X. If there are significant off-diagonal values, then that means that those components are too correlated to estimate.

doug

Goldman, Aaron (NIH/NIMH) [C] wrote:

Thanks. I had one more question now that I'm to mri_glmfit. Based on an

error message I'm getting, it seems something about my design matrix

isn't set up right. I'm inputting a text file for x in which each row

looks like:

1 0 0 1 0 42.35

with the first three numbers being my class variable of interest, the

next two gender, and the last age. It tells me the "matrix is

ill-conditioned or badly scaled, condno = 1e+08," and then prints out

the matrix and aborts. Do you know what I need to do differently for

this to work? Thanks,

-Aaron-

-----Original Message-----

From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu]

Sent: Wednesday, February 14, 2007 11:49 AM

To: Goldman, Aaron (NIH/NIMH) [C]

Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] smoothing question

something like:

mri_surf2surf --s subject --hemi lh --sval input --tval output --fwhm 5

doug

Goldman, Aaron (NIH/NIMH) [C] wrote:

...

Hi, I'm attempting to do thickness analysis based on the guide at:

http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf

For the smoothing part using mri_surf2surf (page 14), I was wondering

what a typical command line should look like.

Thanks,

-Aaron-

---

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

--

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

In order to help us help you, please follow the steps in:

surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Hi Valentina,

if you look on our main wiki page you'll find a bunch of references for cortical surface recon, thickness measurements and surface-based inter-subject averaging.

cheers, Bruce

On Fri, 16 Feb 2007, Durastanti, Valentina (NIH/NINDS) [F] wrote:

Hi,

I used the statistical parametric map provided by Freesurfer to calculate the differences in the regional cortical thickness between two groups. My questions are:

1. Which is the best way to describe this analysis? I have some

difficulties in incorporate it in my statistical analysis. Which references should I use?

2. Where can I read something about the way how the software does this

map and how to exactly interpret them?

Thanks

Valentina