Hi Valentina,

If you are referring to the corpus callosum value from the *h.aparc.annot, this region and the values associated with it are not accurate. Our motivation in including the corpus callosum as a region of interest within our gray matter parcellation atlas was simply as an anatomic placeholder to better delineate the boundaries of the cingulate cortex. As you have mentioned, our anatomic parcellation scheme is for gray matter structures and the corpus callosum is a white matter region and thus intended only as a placeholder, similar to the *h.unknown.label region.

Best regards,

Rahul

---- Rahul S. Desikan rahul@nmr.mgh.harvard.edu

On Thu, 7 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:

Hi, I have two questions:

1. I was wondering if the values of corpus callosum are useful
2. Why the values of the corpus callosum are included in the gray matter

data (.aparc.stat)? I need the volume/area of the corpus callosum and I don't understand if the volume given by the stat file is the whole volume of the corpus callosum

Thanks

Valentina

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

You can use age as a covariate in a regression (make sure to demean them).

doug

On Fri, 15 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:

Hi, I' compared the regional cortical thickness between two groups of subjects using the statistical parametric maps provided by Freesurfer. I was wondering if there is a way to correct the analysis for the age (the two groups of subjects differ for age) or if the Freesurfer already do that. Thanks Valentina

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

I need to compare the regional cortical thickness between two groups of subjects using the statistical parametric maps provided by Freesurfer.

So, I have two classes (patients and healthy volunteers) and one variable (age), if I want correct for age the difference in cortical thickness between these two groups it is enough to write 1, -1, 1 in the contrast vector?

thanks

Valentina

Could you please quantify "almost"? could you also please explain me how can I eventually disable the randomization?

I have another question that I've already put on the list but the answer never came, maybe is not clear enough: I have two classes (patients and healthy volunteers) and one variable (age), if I want correct for age the difference in cortical thickness between these two groups how can I set the contrast vector?

Thanks Valentina

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, December 20, 2006 4:33 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] variability

not quite, but almost. There is some randomization that you can disable if you wanted to On Wed, 20 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:

Hi, I have a question: If I run the same subject twice, without editing, should I aspect to obtain exactly the same results in term of regional and whole cortical thickness or something could change?

Thanks Valentina

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

I have two classes (patients and healthy volunteers) and one variable (age), if I want correct for age the difference in cortical thickness between these two groups it is enough to write 1, -1, 1 in the contrast vector?

thanks

Valentina

-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Friday, December 15, 2006 12:08 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] parametric map

You can use age as a covariate in a regression (make sure to demean them).

doug

On Fri, 15 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:

Hi, I' compared the regional cortical thickness between two groups of subjects using the statistical parametric maps provided by Freesurfer.

I

was wondering if there is a way to correct the analysis for the age

(the

two groups of subjects differ for age) or if the Freesurfer already do that. Thanks Valentina

---

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

Using the fwhm option requires a subject because it needs to take into accnt the surface area. ico7 is not a true subject in the freesurfer sense. However, you should have fsaverage in your distribution, and that is the same as ico7.

The conversion from fwhm to niters is here:

gstd = fwhm/sqrt(log(256.0)); //1.14 is a fudge factor based on empirical fit of nearest neighbor niters = floor(1.14*(4*PI*(gstd*gstd))/(7*avgvtxarea) + 0.5);

The avgvtxarea is the average area for the given subject.

doug

On Thu, 4 Jan 2007, Roberto Toro wrote:

Hi!

I'm trying to smooth thickness data using mri_surf2surf. The thickness vectors are mapped onto ico7, and I would like to smooth the thickness there (ico7). But when I add the --fwhm option to mri_surf2surf (equivalent to --fwhm-trg), mris_surf2surf looks for a real subject called "ico" (ie $SUBJECTS_DIR/ico/surf/lh.white) instead of the oversampled icosahedron...

This is the type of command I'm using (with freesurfer-Darwin-tiger- stable-pub-v3.0.2, mac os 10.4.8):

mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject ico --trgicoorder 7 --fwhm 30 --trgsurfval /Users/roberto/Desktop/bertest-lh.mgh --trg_type mgh

without --fwhm everything goes ok, but including it produces at the end an error like this:

(...) MRISread(/freesurfer/subjects/ico/surf/lh.white): could not open file No such file or directory ERROR: could not read /freesurfer/subjects/ico/surf/lh.white

It looks for a subject ico. I think that I could use --fwhm-src to do the smoothing on bert/lh.white, but then different brain sizes would have different fwhm values after mapped over ico7...

Is there a way of giving an absolute path to the surface used for smoothing? (to /Applications/freesurfer/lib/bem/ic7.tri). Am I doing something wrong?

A last little thing.... how is the number of iterations (à la --nsmooth) computed from the given fwhm?

thanks in advance! (and have a happy new year :)

roberto

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