Re: [Freesurfer] Log transformation vertex-wise

you just want to compute the log of the voxel values in a volume? You can use fscalc

On 9/8/2020 6:30 AM, Jose Graterol wrote:

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Hey Tim,

thanks for the quick response and for the script. I will try that.

Best,

José

On Tue, Sep 8, 2020 at 11:07 AM Tim Schäfer <ts+ml@rcmd.org mailto:ts%2Bml@rcmd.org> wrote:

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Hi José,

most likely there is an easier way to do this with some FreeSurfer
command that others can suggest (and I am not aware of), but I
would do it in R with this script:
https://gist.github.com/dfsp-spirit/ccdc8c5efb0cff2ba5b139190bbfb397

Best,

Tim

> On September 8, 2020 at 10:25 AM Jose Graterol
<gpjosealberto13@gmail.com <mailto:gpjosealberto13@gmail.com>> wrote:
>
>
>         External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I have a technical question for which I have not yet found the
answer.
> First, I am running FreeSurfer stable-pub-v6.0.0-2beb96c on
CentOS 7.
>
> Now to the question: is there a way to apply, say, a logarithmic
> transformation vertex-wise? For example, while doing a
whole-brain analysis
> for cortical thickness with mri_glmfit it would calculate
everything with
> the logarithmic value instead of mm.
>
> If this is not implemented, do you have an idea of how I could
achieve
> this? Perhaps extracting the matrix with the values of each
vertex and
> reading it in Matlab?
>
> Thanks in advance.
>
> José
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am
Main, Germany

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