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Subject:

Re: cluster failure article

From:

"Harms, Michael" <[log in to unmask]>

Reply-To:

Harms, Michael

Date:

Thu, 21 Jul 2016 19:35:35 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1 lines)



Although, depending on the duration of the prescan calibration, there are

still transients in the BOLD related to (e.g.) the onset of the auditory

stimulation, or appearance of a visual fixation cross-hair, and these

transients may last longer than just 5 frames.  I believe that Tim Laumann

had a poster on this effect at the 2015 OHBM.



cheers,

-MH



--

Michael Harms, Ph.D.



-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.Tel: 314-747-6173

St. Louis, MO  63110Email: [log in to unmask]









On 7/21/16, 2:28 PM, "SPM (Statistical Parametric Mapping) on behalf of

Angstadt, Mike" <[log in to unmask] on behalf of [log in to unmask]>

wrote:



I believe this is handled by the 1000 Functional Connectomes project

already. They’ve indicated that they dropped the first 5 scans from all

sites data prior to releasing it, so the data that would have been

downloaded and used for the Eklund et al analysis should have already had

those first few scans trimmed off.



Mentioned here:

http://www.nitrc.org/forum/message.php?msg_id=6213

and here:

http://www.nitrc.org/docman/view.php/296/716/fcon_1000_Preprocessing.pdf



-Mike



--

  Mike Angstadt

  Research Computer Specialist / PANLab Lab Manager

  Department of Psychiatry / University of Michigan

  (734) 936-8229







From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On

Behalf Of John Ashburner

Sent: Thursday, July 21, 2016 2:00 PM

To: [log in to unmask]

Subject: Re: [SPM] cluster failure article



Hi Cyril,

I'm struggling with the comment system for the blog (possibly due to my

version of FireFox).  This is what I had intended to say:

In relation to the bit that says "some cases with the 1-sample t-test

where the nonparametric approach had elevated FWE, due to skew in the

data", it is important to stress that the first few scans of each fMRI run

should not be included in the analyses.  It is reasonable to guess that

the skewing is due to these images being systematically different from

those collected later in the run when a steady state has been reached.



All the best,

-John



On 21 July 2016 at 17:14, PERNET Cyril <[log in to unmask]> wrote:

Dear all,



There is now a blog post explaining in a different way the results the the

Eklund et al. paper. We tried to be as didactic as possible



http://www.ohbmbrainmappingblog.com/blog/keep-calm-and-scan-on



Keep Calm and Scan On

www.ohbmbrainmappingblog.com

BY: JEANETTE MUMFORD, CYRIL PERNET, THOMAS YEO, LISA NICKERSON, NILS

MUHLERT, NIKOLA STIKOV, RANDY GOLLUB, & OHBM COMMUNIATIONS COMMITTEE (IN

CONSULTATION WITH THOMAS NICHOLS)   In recent weeks a...



Cyril





________________________________________

From: SPM (Statistical Parametric Mapping) <[log in to unmask]> on behalf

of PERNET Cyril <[log in to unmask]>

Sent: 19 July 2016 07:50:43

To: [log in to unmask]

Subject: Re: [SPM] cluster failure article



Yann,



The paper is quite clear, if you set p higher than 0.001 then your blobs

becomes to big (under the null) for random field theory to be able to give

you the right cluster size threshold and the nominal type 1 FWER is higher

(ie you don't control as expected). This doesn't matter if its a one

sample t-test or a contrast from an ANOVA, it is still wrong (see 1994

paper from K Friston).



Dr Cyril Pernet

Senior Academic Fellow

CCBS / Edinburgh imaging



Sent from my HTC mobile phone



----- Reply message -----

From: "Yann Quidé" <[log in to unmask]>

To: "[log in to unmask]" <[log in to unmask]>

Subject: [SPM] cluster failure article

Date: Tue, Jul 19, 2016 01:25



Hi all,



Just to jump on Mike's comment on wether an initial p=0.005 (+

cluster-wise correction) would be ok or not?



I understand there are less risks to report false positive blobs using

p=0.001 as an initial threshold, and the need to (at least) use a strict

p=0.001 (+ cluster-wise correction) when looking at within group

activation and/or correlation. However, would it become a problem to use

an initial threshold of p=0.005 (+ cluster-wise correction) when looking

at, say for instance, 2x2 (between groups) ANCOVAs with clinical

populations? This more liberal threshold will impact spatial sensitivity,

but will it impact the validity of the findings?



Thanks.



Yann





On 14 Jul 2016, at 6:31 pm, Mike <[log in to unmask]> wrote:



> Thanks for everyone's replies. However, I believe that many researchers

>who use fMRI analysis software are not with a firm statistical

>background, just like me. For practical reasons, we need a "guideline,"

>if any, to control multiple comparisons problem. Concerning cluster-wise

>thresholding, below is what I would follow according to Woo et al., 2004

>and the recent cluster failure paper in PNAS, but I hope some erperts

>here can comment a bit.

>

> (1). For SPM and AFNI 3dClustSim users, the first arbitrary

>cluster-forming threshold (CFT) is suggested to be not too lenient. 0.001

>is good, but 0.01 is definitely poor (I have no idea if 0.005 is ok or

>not?). Then you can report clusters that survive a FWE-corrected p<.05 at

>the cluster-wise level (but can I report FDR-corrected p<0.05?). The

>commonly used "P = 0.001 uncorrected with a k of 10 voxels" should be

>abandoned.

>

> (2). The commonly used "P = 0.001 uncorrected with a k of 10 voxels"

>should be abandoned (but it seems that many people still use it...).

>

> Besides, I have a naive question: since cluster-extent based

>thresholding might be more problematic, why don't we just stick on

>voxel-wise thresholding?

>

> Mike



The University of Edinburgh is a charitable body, registered in

Scotland, with registration number SC005336.



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