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Dear Dr. Douglas,

Thank you so much for your detailed response.

The simulation here is to get the probability of a maximum cluster that size or larger in the cached CSD files. It checks the probability of  the cluster size but have nothing to do with the analysis metrics that I have used. Do I understand correctly?

Best regards,

Ting Li

On Mon, Dec 2, 2019 at 11:57 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

On 12/2/2019 11:58 AM, Ting Li wrote:

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Dear Dr. Douglas,

Thank you so much for your quick response! You saved my half life.

From the introduction of clusterwise correction for multiple comparisons, I have a few questions.

1, What is the null hypothesis here ?

In the tutorial, the null hypothesis is that there is no effect of age (age slope = 0)

2, What is a z map? Do you mean synthesize cortical datasets?

A z-map is just a map where all the values are from a gaussian distribution with mean=0 and stddev=1. This just assigns a random z-value to each vertex on fsaverage

3. Smooth z map, what FWHM do you use, if it is not consistent with my FWHM, how will it affect the results?

The FWHM comes from an estimate from the residuals of the analysis. The residuals are everything that does not fit the linear model and represent noise. We use the residuals to estimate the underlying smoothness (FWHM),

4, Threshold z map, what does level mean? Does it mean the vertex p-value?

Basically, it is the vertex p-value, but we use  the "sig" = -log10(p). You also have to specify the sign. If you have an a priori hypothesis about the direction, then you can specify pos (positive) or neg (negative). If you do not have an a priori hypothesis, then use abs (for absolute, for an unsigned test).

Clusterwise Correction for Multiple Comparisons

To perform a cluster-wise correction for multiple comparisons, we will run a simulation. The simulation is a way to get a measure of the distribution of the maximum cluster size under the null hypothesis. This is done by iterating over the following steps:

1. Synthesize a z map

2. Smooth z map (using residual FWHM)

3. Threshold z map (level and sign)

4. Find clusters in thresholded map

5. Record area of maximum cluster

6. Repeat over desired number of iterations (usually > 5000)

Thank you so much!

Best regards,

Ting

On Mon, Dec 2, 2019 at 10:20 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

That will use the pre-computed ("cached") CSD files distributed with FreeSurfer. This used 10,000 iterations.

On 12/1/2019 11:34 PM, Ting Li wrote:

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Dear Freesurfer Expert:

I have used the simulation code as show below: 

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

My question is how many iterations are done during this simulation? I didn’t specify the iteration number.

Why I didn’t have the csd file? 

Thanks a lot for your response!

Best regards,

Ting

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