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 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 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/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 *