that looks right; I don't think you need a 2nd --thfile (but does not hurt it).
On 1/3/2022 3:27 PM, Laura Willers de Souza wrote:
External Email - Use Caution
Dear Douglas,
Once again, thanks so much for the reply!
About the mask, I just don't put anything or put "nomask"?
With your suggestions, the command looks like this:
mri_fdr --fdr .05 --pos --thfile $SUBJECTS_DIR/hipposubfields.lh.T1.v21.CU_CI.glmdir/sig.table.dat --i $SUBJECTS_DIR/hipposubfields.lh.T1.v21.CU_CI.glmdir/group.diff.CU_CI/sig.mgh nomask hipposubfields.lh.T1.v21.CU_CI.mgh --thfile $SUBJECTS_DIR/hipposubfields.rh.T1.v21.CU_CI.glmdir/sig.table.dat --i $SUBJECTS_DIR/hipposubfields.rh.T1.v21.CU_CI.glmdir/group.diff.CU_CI/sig.mgh nomask hipposubfields.rh.T1.v21.CU_CI.mgh
Do you think this is correct?
As it was before (without the input to --thfile) it was giving the following error:
I believe that with these fixes it should work fine, right?
Thank you so much again!
Best, *Laura Willers de Souza *
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
*De:* Douglas N. Greve dgreve@mgh.harvard.edu *Enviado:* domingo, 02 de dezembro de 2022 *Para:* Laura Willers de Souza laura.w.desouza@hotmail.com *Cc:*freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Assunto:* Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala
Dear Douglas, Thanks so much for your answer. Could you check if the following commands to perform ROI analysis withGLM 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 replacelh 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.mghlh.mask.mghhipposubfields.lh.T1.v21.CU_CI.mgh --no-log10p --icontrast/rh.sig.mgh rh.mask.mghhipposubfields.rh.T1.v21.CU_CI.mgh--no-log10pFor this one, you don't need a mask. Also, don't use --no-log10p (theoutput 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 herehttps://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52203.html <https://secure-web.cisco.com/1KedI8-SZfRiRhwkEfi_d25zdjoR6A_msh6cCPc1dap84Ly06bbEc5bmznRW4Rvt0wFBsQtYqwHmWW24gBU1aRY-BR47jXkcx0_vNDDfrV8UUOWWWGAne-Knqsq8SspWcL9TwmNDYrhIjVsf2IoRd-F6polEPsdbrO8egzIe4FTCyzPPCKP_vqcm0CxBLUVzgmPbz9s6k24V1m4gITDRkwsBoy_8b63WcNCxaEsdBsKSaLS5V9V1RRcMzQVCvvRsD76qHheatdwoXRn_ksHC4jTcfRkZcDx5lImgGddIHL9q477hb_njEu6aLcj8SAAnS/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52203.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 *
