External Email - Use Caution

Dear Tim,

Thank you for your reply. I used these two commands and now it seems that everything worked fine:

1) cd glmdir/contrast fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh

2) mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 --sum test.output

After using the second command, I can open the test.output file and see the mean Cohen's D of each significant cluster. Is correct the second command?

mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 --sum test.output

Thank you very much.

Best regards,

Steve.

El sáb., 25 dic. 2021 15:57, Tim Schäfer ts+ml@rcmd.org escribió:

    External Email - Use Caution

Hi Steve,

what exactly do you mean by unable to open? What happens if you try to load it as an overlay for fsaverage in FreeView? Is there any error message if you try to open it?

Best,

Tim

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

...

On 12/22/2021 5:02 PM Steve Petersen marfneuro@gmail.com wrote:

External Email - Use Caution

Dear Freesurfer experts,

I would really appreciate it if anyone can give me some guidance about

this

...

question that I posted a few days ago. I conducted a One-way ANOVA and

now

...

I would to report the Cohen's D effect size for each pairwise comparison (t-tests). For that purpose, I estimated the Cohen's D effect size of significant clusters using the suggested command <

https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqd...

...

:

fscalc gamma.mgh div rstd.mgh -o cohensd.mgh

Now, I get the cohensd.mgh file but I am not able to open this file. How can I see the particular effect size of each significant cluster included in the sig.cluster.summary file?.

Thank you very much in advance for your time!

Best regards,

Steve,

El mié, 15 dic 2021 a las 19:14, Steve Petersen (marfneuro@gmail.com) escribió:

...

Dear Freesurfer experts,

I am attempting to estimate the Cohen's D effect size of significant clusters using the suggested command <

https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqd...

...

:

...

fscalc gamma.mgh div rstd.mgh -o cohensd.mgh

Now, I get the cohensd.mgh file but I am not able to open this file.

How

...

...

can I see the particular effect size of each significant cluster

included

...

...

in the sig.cluster.summary file?.

Thank you very much for your help!

Best regards,

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

https://secure-web.cisco.com/1DzWVfD7aS3RdSncH3YwQ3Gj-hgoNwquNSuAofwpNP31cDy...

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Yes, that looks correct

On 12/25/2021 11:07 AM, Miguel Ángel Rivas Fernández wrote:

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Sorry, I wrote this previous email from a different adress because I did not receive emails from the freesurfer's support list 😅

Thank you!

El sáb., 25 dic. 2021 17:01, Miguel Ángel Rivas Fernández miguelrivasfdez@gmail.com escribió:

Dear Tim,


Thank you for your reply. I used these two commands and now it
seems that everything worked fine:


1) cd glmdir/contrast  fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh

2) mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0
--sum test.output


After using the second command, I can open the test.output file
and see the mean Cohen's D of each significant cluster. Is correct
the second command?

mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0
--sum test.output

Thank you very much.


Best regards,

Steve.

El sáb., 25 dic. 2021 15:57, Tim Schäfer <ts+ml@rcmd.org
<mailto:ts%2Bml@rcmd.org>> escribió:

    External Email - Use Caution

    Hi Steve,

    what exactly do you mean by unable to open? What happens if
    you try to load it as an overlay for fsaverage in FreeView? Is
    there any error message if you try to open it?

    Best,

    Tim


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

    > On 12/22/2021 5:02 PM Steve Petersen <marfneuro@gmail.com>
    wrote:
    >
    >
    > External Email - Use Caution
    >
    > Dear Freesurfer experts,
    >
    > I would really appreciate it if anyone can give me some
    guidance about this
    > question that I posted a few days ago. I conducted a One-way
    ANOVA and now
    > I would to report the Cohen's D effect size for each
    pairwise comparison
    > (t-tests). For that purpose, I estimated the Cohen's D
    effect size of
    > significant clusters using the suggested command
    >
    <https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html>:
    >
    >
    > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh
    >
    > Now, I get the cohensd.mgh file but I am not able to open
    this file. How
    > can I see the particular effect size of each significant
    cluster included
    > in the sig.cluster.summary file?.
    >
    > Thank you very much in advance for your time!
    >
    > Best regards,
    >
    > Steve,
    >
    > El mié, 15 dic 2021 a las 19:14, Steve Petersen
    (<marfneuro@gmail.com>)
    > escribió:
    >
    > > Dear Freesurfer experts,
    > >
    > > I am attempting to estimate the Cohen's D effect size of
    significant
    > > clusters using the suggested command
    > >
    <https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html>:
    > >
    > >
    > > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh
    > >
    > > Now, I get the cohensd.mgh file but I am not able to open
    this file. How
    > > can I see the particular effect size of each significant
    cluster included
    > > in the sig.cluster.summary file?.
    > >
    > > Thank you very much for your help!
    > >
    > > Best regards,
    > >
    > >
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    >
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