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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 wrote:

    External Email - Use Caution

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

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

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Yes, that worked. Thank you.

Douglas N. Greve dgreve@mgh.harvard.edu schrieb am Di., 8. Sep. 2020, 17:04:

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:

    External Email - Use Caution

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 wrote:

...

    External Email - Use Caution

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

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

---

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

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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