On 1/4/2022 2:42 PM, Laura Willers de Souza wrote:
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The command worked fine! But, in the end, the file that contains the thresholds for each of the ROI (first image below) ends up being replaced by the FDR value (second image below), which is not very good, because this information ends up getting lost.
I don't understand what you mean. The value in the file is the threshold that you would use to divide your ROIs into significant vs nonsig groups in a way that meets the FDR criteria; in your case, it looks all but subiculum will pass. Or are you looking for an FDR-corrected p-value for each ROI?
Is there any way to save the FDR value in another file and not in the same one where the p-values of the ROI are?
And is it possible to visualize the ROIs with the significance scale in freeview? I tried to overlay the sig.mgh file over the inflated surface and also the mri_fdr output.mgh file, but it didn't work.
That definitely will not work.
What should I do to make this work?
You have to convert the table into a map. You can get a tool to do this from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/table2map username 'guest' password 'collab' I'm not totally sure it will work as a stand-alone. You might have to download the development version of FS to get it. Specify the subfields segmenation as the --seg option.
Thank you so much again, *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:* terça-feira, 4 de janeiro de 2022 15:21 *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 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:
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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 mailto:dgreve@mgh.harvard.edu *Enviado:* domingo, 02 de dezembro de 2022 *Para:* Laura Willers de Souza laura.w.desouza@hotmail.com mailto:laura.w.desouza@hotmail.com *Cc:*freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto: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 <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 *The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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