Hi Sourena

yes, that is true. If you are doing a jacobian analysis you probably want to either turn the metric preservation term all the way up (or just terminate the warp after the rigid rotational alignment) and analyze the curvature, or all the way down so that everything is in the jacobian. Or I guess you could include the curvature residuals in your model.

I haven't done much of this personally, so others may have a more informed opinion.

cheers Bruce

On Sat, 10 Nov 2012, Sourena Soheili-Nezhad wrote:

Hi Bruce

Thanks, it worked. A follow-up question: I am performing multivariate analysis of the jacobian to cluser co-variating cortical patches which shrink/expand together. So, is it correct that if I omit/decrease the jacobian penalty term in the spherical registration step then I will get more variance (and more information), since the folding patterns will register more freely? Does this kind of extra variance in the jacobian sound legitimate?

Thank you for your time, Sourena

On 11/10/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Sourena

there are matlab scripts for reading/writing curv files, but you are probably better off stuffing things into a "volume" and saving it in .mgz format using MRIwrite.m

cheers Bruce On Sat, 10 Nov 2012, Sourena Soheili-Nezhad wrote:

...

Hello Freesurfer expert community I have been analyzing the jacobian values outside freesurfer by exporting it to ascii format. Now, I have come up to vertex-wise statistical values which I wish to project on the study surface. Reading the list, I have created an ascii with each row representing <#vertex> <X> <Y> <Z> <scalar value>. This file is only viewable in tksurfer (not freeview) and the problem is that after using the curv_to_val script in tcl, the values outside [-2,2] (the blue and red colors) don't get updated when I load another file (they "freeze" on the previously loaded values). Any suggestion on a better way to view the ascii .curv format is highly appreciated. Also, does there exist any publicly-available I/O for writing binary .curv format so I can import it to freeview as well?

Thanks, Sourena Soheili-Nezhad

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