External Email - Use Caution
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:
External Email - Use CautionDear 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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