External Email - Use Caution        

Hi Dan,

excuse the late response; regarding your remaining questions:

1)
This sounds correct to me, pcor is the corrected threshold that can be applied to the sig.mgh files.

2)
If I am not mistaken, the spval file should be equivalent to the sig file, at least for two-sided tests (the default), and with the exception that the sig file is at the -log10 scale and may have a sign attached to it to indicate the direction of effects. Since the spval file is, if I recall correctly, plain p-values, one could use the pth value to set a threshold for this file.
This means that we don't transform the p-values to achieve multiple comparison correction, but instead use a stricter threshold that controls the FDR2 at the 0.05 level.

Best regards,

Kersten

On Thu, 2024-05-02 at 14:25 -0400, Dan Levitas wrote:
> CAUTION: This email originated from outside of DZNE. Do not click
> links or open attachments unless you recognize the sender and know
> the content is safe.
> ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig
> beim Anklicken von Links oder Öffnen von Anhängen
>
>
>         External Email - Use Caution
>
> Hi Martin,
>
> Thanks for the response!
>
> After my original post I went through things more carefully based on
> my two original two questions and made a follow-up post here
> (https://secure-web.cisco.com/19ziz4OS6HL3HuOwgHLcrspNdIovd6NTUuIdpJ-
> mDFOvCAyWs2kPDBlUfdSjbT8fclH9nL7GIu1MIetcqQwD2s6-5_CVIvLCVZ6V0NHWw83d
> N7z4bxX8JjTlz4F5ySCoY2Hn-W5BAu721AwV6QhGaqXBgr32xC1Hj1I1rKrQTyQlP1eIg
> 9Gw3g91iL5agTdIsuQfhuCLS5fDVYGvek_rQh6ZDb-tutbyEWAlZ7ea8enpBmRCBEaMTH
> GC1pIKz_9aNARmcDOkjf-Znc91tyjFrHT7suqi_CYkPmpMZGFa4URHOcVwpqegNeEb-sV
> 6X4R-YqiERw6UNMAaIXGQAFjAQ4Q/https%3A%2F%2FMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.mail-archive.com%2Ffre
> esurfer%40nmr.mgh.harvard.edu%2Fmsg76783.html) with two final
> questions. The gist of these is that I’m unsure how to apply my
> multiple comparisons (for both hemispheres) to the analysis and
> subsequent visualization. Do you have any guidance on how I should
> proceed.
>
> Much appreciated,
>
> Dan
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> The information in this e-mail is intended only for the person to
> whom it is addressed.  If you believe this e-mail was sent to you in
> error and the e-mail contains patient information, please contact the
> Mass General Brigham Compliance HelpLine at
> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline>
> .
> Please note that this e-mail is not secure (encrypted).  If you do
> not wish to continue communication over unencrypted e-mail, please
> notify the sender of this message immediately.  Continuing to send or
> respond to e-mail after receiving this message means you understand
> and accept this risk and wish to continue to communicate over
> unencrypted e-mail.