On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote:
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Dear Freesurfer experts,
I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
I have followed the group analysis tutorial ( *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#GLMAnalys... https://secure-web.cisco.com/1pRD_UxgiIfPoYGdD-txQXbrB2PxuCy8sHKMjDgu-jv8mYA8xtQi6fT8t-cAQUuGG87avFRj2LEhHAIJlc1Awzxm1fIYMMnvHXmPOwiLnPZbiUN7Cyo5Mxqi2uNf8dw0M2_AMgq4opPKNVEeC65234qGSj1uEo4GtDxAL7c2MU4wI42FVRcau9LBBIWOQtTM_FMAGfwE7I5Td_KdKo1ppb_aUikrW8Sifb5gQuDAN-9u6FuzGdQ_I83Nns91USYKlhryBhDwhd2XauXyZHk9F9A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis%23GLMAnalysis.28mriglmfit.29 ), where it is suggested to do a Z Monte Carlo simulation with the following command: mri_glmfit-sim \ --glmdirlh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces However, I have two questions regarding this issue:
- I would like to know whether is it correct to use for example
--cache 3 or 2 instead of 4. Is it recommended?
Is this a thickness analysis? If so, 3 is probably ok, but 2 is too low; also depends on the smoothing level.
- Is it better to use, instead of the above Z Monte Carlo simulation
command, a permutation with the following command?: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --perm 1000 4.0 abs \ --cwp 0.05\ --2spaces \ --bg 1
The permutation will be more accurate, but at a threshold of 4, it probably won't matter much. But the good thing about permutation is that you can drop the threshold to 3 or 2 or even 1.3, and it will still do the right thing.
Is it appropriate to use any of both? I do not know which is more recommended or whether both are adequate so I can simply choose, for example, the first one.
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
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