Thank you, Doug.

Regards

Virendra

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, October 12, 2016 11:45 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Should I use no-adjust in mri_surfcluster

If all you want to do is fdr correction you can use this program:

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr

On 10/10/2016 07:31 PM, Mishra, Virendra wrote:

Hi, FreeSurfer Users.

I am comparing cortical thickness of 2 groups controlled for certain

variables of no interest.

My contrast matrix is

1 -1 0 0 0 0 0 0 0 0 0 0 to check for group 1 thickness > group 2

thickness

I get my sig.mgh and I want to run mri_surfcluster command to correct

for FDR.

I am confused as to whether I should use -no-adjust in

mri_surfcluster. According to the help mri_surfcluster

(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster) :

I have to use -no-adjust if my sig.mgh is not a log(10) map and

sig.mgh was created using a one-tailed test.

Since my contrast is group1>group2 ; I am thinking my sig.mgh is a

log(10) but a one-tailed. Hence I have to use -no-adjust.

But then again, mri_glmfit

(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit) says if #of

rows in Contrast matrix is 1 (which is true in my case), then the

F-test reduces to a two-tailed t-test which means I should not use

-no-adjust.

I would appreciate any response regarding this.

Thanks

Regards

Virendra

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Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.

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