Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 of this paper

False positive rates in surface-based anatomical analysis
Douglas N. Greve a, b, * , Bruce Fischl a, b

On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote:

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Dear Douglas, 

So, as far as I understand you, if I use a smoothing of 15 I can use a --cache of 2 in thickness analysis, but I should use a higher --cache for volume, such as 3. Is that correct? 

And would you recommend me using another smoothing level? 

Thank you very much for your help. 

Kind regards, 

Agurne

El mar, 9 feb 2021 a las 17:44, Douglas N. Greve (<dgreve@mgh.harvard.edu>) escribió:

That is ok for thickness, but not for volume

On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote:

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Dear Douglas, 

I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adequate at least for volume analyses?

Thank you very much.

Best regards, 

Agurne

 

Neuropsychology of Severe Medical Conditions Research Team

Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education 

University of Deusto

neurolab.deusto.es

 

Avda. de las Universidades 24, 

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)

El mar, 9 feb 2021 a las 15:46, Douglas N. Greve (<dgreve@mgh.harvard.edu>) escribió:

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#GLMAnalysis.28mriglmfit.29 ), where it is suggested to do a Z Monte Carlo simulation with the following command: 

mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces

However, I have two questions regarding this issue:

1) 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.

2) 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

neurolab.deusto.es

 

Avda. de las Universidades 24, 

48007, Bilbao (Spain)

Phone: +34 944139000 (ext. 3015)

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