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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 ?

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

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

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

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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