FW: Number of iterations with --cache flag - Freesurfer

31 May 2018

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Hey Doug,
thanks for the suggestions!
I have some follow-up questions, also regarding your recently published paper about false positive rates (https://www.sciencedirect.com/science/article/pii/S1053811917310960).
1) What will the difference be between 1000 and 10,000 iterations? I read in the tutorial that >5000 iterations are recommended?
2) In your paper you write that permutation requires that data is exchangeable across subjects and that age effects may be a problem. In our study we want to compare adolescent patients with ADHD and conduct disorder with typically developing adolescents. In this context, data would not be exchangeable across subjects, right? Could we still use permutation?
3) When using the CFT thresholds with Monte Carlo simulation you recommend in your paper, do you still only report clusters with CWP<.05 or is the CWP less important when using stricter thresholds?
4) Which surface area do you use in your paper? White or pial? Is one "better" to use than the other?
Thank you so much for your input!
Best, 
Lea Backhausen
------------------------------
Lea Backhausen
Research Assistant
Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany
http://www.uniklinikum-dresden.de
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Message: 1
Date: Tue, 29 May 2018 12:06:01 -0400
From: Douglas Greve dgreve@mgh.harvard.edu
Subject: Re: [Freesurfer] FW: Number of iterations with --cache flag
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 72d462b2-5f9d-f2a7-e3fd-0c60e24f96de@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
Actually, I think 1000 is probably fine. Also, you may wan to use 
permutation since the monte carlo correciton tends to be too liberal. 
here are instructions
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0P...
On 5/29/18 11:37 AM, Backhausen, Lea wrote:
...
Sorry, found it! It?s 10000 as indicated in the sig.cluster.summary file.
Best,
Lea Backhausen

Lea Backhausen
Research Assistant
Department of Child and Adolescent Psychiatry, Faculty of Medicine of 
the TU Dresden, Germany
http://www.uniklinikum-dresden.de http://www.uniklinikum-dresden.de/
*From:*Backhausen, Lea
*Sent:* Tuesday, May 29, 2018 4:53 PM
*To:* 'freesurfer@nmr.mgh.harvard.edu'
*Subject:* Number of iterations with --cache flag
Dear FreeSurfer Experts,
I am wondering how many iterations are run in the precomputed Z Monte 
Carlo simulation when using the --cache flag with mri_glmfit ?sim.
Sorry if this has been documented somewhere, I cannot find it ? can 
anyone direct me to the right page?
Thank you for your help!
Best
Lea Backhausen

Lea Backhausen
Research Assistant
Department of Child and Adolescent Psychiatry, Faculty of Medicine of 
the TU Dresden, Germany
http://www.uniklinikum-dresden.de http://www.uniklinikum-dresden.de/

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