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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-mDFOvCAy...) 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
Hi Dan,
I have not worked with this code in a decade, but Kersten in my group maintains our R package of it ( see https://github.com/deep-mi/fslmer ). I will bring this to his attention.
Basically I think you determine the joint p-threshold across hemispheres and convert it to FreeSurfer ( - log10 pth) and use that value as a threshold when plotting the original p-values. That way you only need one threshold for the full plot, rather than two different ones (or the more pessimistic of the two).
Also you may be interested in our whippersnappy python tool to generate nice looking screenshots of the surface overlay: https://github.com/Deep-MI/whippersnappy
which is pip installable.
Best, Martin
On 2. May 2024, at 20:25, Dan Levitas djlevitas208@gmail.com wrote:
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/1sMx-dupqFSyAsxsQl8ukXwR4v0-vTUkX2pc5vfwlqp166r...) 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
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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:
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External Email - Use CautionHi 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%2Fwww.mail-archive.com%2Ffrehttps://secure-web.cisco.com/1kchikxmLpZHWE7XyYZnsTVecuArk_jBroxFyw7kHlB13QmW_K5rCcUJu0VDxm94RT9VS9WKD6NrRonkI--lWNVR1uqBR0_sMqUVdBm8QOVeZKZbvaFqTz601ha-o69g9Q2PaqhdBRe4oob74lWrVwMrlpoAeplWjeTOpGGqPeXNPGYSH_HXJOwBGbk4NZ-QNUMAdf6-H_t7sC1w3yCnLJzyrnmp7LqG-Ip8OVvvid4gJ_jkxblfV1ZDSguHV02i-JUEd7NU7zp1d7LkDiAUr-4eKMDI55nuWiesN3NAfUyuo24pmiFDec78xRFmV3kY-/https%3A%2F%2Fwww.mail-archive.com%252Ffre 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
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