On 12/20/2021 9:20 PM, Laura Willers de Souza wrote:

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Dear Douglas,

Thanks so much for your answer.

Could you check if the following commands to perform ROI analysis with GLM are correct?

*1.* Create the table with the volumes of the hippocampal segmentation (1 command for each hemisphere - only replace lh with rh):

asegstats2table --statsfile hipposubfields.lh.T1.v21.stats --fsgd CU_CI.fsgd\ --meas volume \ --all-segs \ --tablefile hipposubfields.lh.T1.v21.CU_CI.dat

*2.* GLM Analysis – DODS (1 command for each hemisphere - only replace lh with rh):

mri_glmfit \ --table hipposubfields.lh.T1.v21.CU_CI.dat \ --fsgd CU_CI.fsgddods \ --C group.diff.CU_CI.mtx \ --glmdir hipposubfields.lh.T1.v21.CU_CI.glmdir

*3.* Correction for multiple comparisons – FDR:

mri_fdr --fdr .05 --pos --thfile --i contrast/lh.sig.mgh lh.mask.mghhipposubfields.lh.T1.v21.CU_CI.mgh --no-log10p --i contrast/rh.sig.mgh rh.mask.mghhipposubfields.rh.T1.v21.CU_CI.mgh --no-log10p

For this one, you don't need a mask. Also, don't use --no-log10p (the output of mri_glmfit is in log10p). --thfile needs an argument (eg, threshold.dat)

Are these commands correct?

Another question, in this type of analysis is image smoothing common? Like was done here https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52203.html https://secure-web.cisco.com/1we0tWxEcmAWpL06CsQ9vqTCkjuPHErSGyrotLh2MGxv3lQ9oLaGS5mPuSAbSeU01BLaT_kHew9Lf3DdE0p8vh0IaIEDCGwKQF1Ulcz8LxixmB8KkLj-1Vi6H7ciW9Rl7qpnwB3OaaAKyp1s2kuKMToWAMnsnCFVDfVBIu4wUzjLINbCXQaahGk7iCPSUCIKvCK-BA8dJGmeP8tow2PcpEF-f9eZm8laYLJJ7x8fL9lIqe_bHBt2kwhAII8fd2wBoAtwHL0Jx0YNP2NdY7WNZFwGGKG7LnbRBFoqHmeVCKsZZ1_M2y-58G2Xw3B7YsD0l/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52203.html

No, it would make no sense here because this is an ROI analysis

Thank you so much again!

Best regards, *Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

• Porto Alegre/RS - Brazil