Get the sign from the gamma.mgh file
On 6/2/2022 12:15 PM, Thalhammer, Melissa wrote:
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Hey guys, I am working with Freesurfer 7.1.1. to compare two groups' cortical thickness values within Desikan-Killiany ROIs while correcting for (mean-centered) sex. I have extracted thickness values within ROIs into a txt using /aparcstats2table /and have then used /mri_glmfit --table Study.txt /to perform group analysis on thickness values within ROIs.
For a future analysis, I want to extract the t-statistic (corrected for sex) per ROI into a txt/csv. This post (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06048.html https://secure-web.cisco.com/1AckjDBImCzyv658H_aa2jCFZOZfDab0c5vz4aXbS0uIdrb8Gekj7fJ5DdgU9YMG1BpHumBFVUxxx489KTBlTQP6d1owS9vPdrbLijofnXjXCKgIUq2VLnKAiPqnM7r6DcpCNXRMzu8xEE-Y3nK4YlZOx_SvEFDY4_MD92o4HsP8X4OhL3z7DKROb_reW7tTasxLNug_VogpuTd6UHZlbMQOSOSXYNOjCq1QHnPgbzrruwrpkBBMSCYC4YbDlzKvug6qwTAM2_VGqjWFTEgw0uThSmvR2sHKfoFa59-Xy5Iuj1s2FMz_zddZbhv0NIvdaql7-ocvWqmb8MsDyrvKzmg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg06048.html) states that F.mgh stores the F-ratio, which is F=t^2, so t=sqrt(F). So, in principle, I should be able to calculate t from my F.mgh file. However, using the squareroot will only yield positive values. I have run a t-test on my data (using simply Python scipy.stats.ttest_ind): the values are actually the same as using sqrt(F), but signs differ (since t calculated from F can only be positive).
Is there a better way to calculate a t-statistic while regressing out a covariate within ROIs? Many thanks in advance, Melissa
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