External Email - Use Caution
Dear Dr. Douglas,
Thank you so much for all the answers. I have two more questions.
1, When the Monte Carlo simulation is doing, how does one simulation is
done?
- synthesize z map (synthesize z map for how many subjects?)
- smooth z map (You have mentioned the FWHM comes from an estimate from
the residuals of the analysis, which analysis? or the way we process the
real data with the command mris_preproc with FWHM value? )
- threshold z map (Does it mean a GLM analysis so we can have threshold
z map?)
2, When we reference to the CSD files in freesurfer, will it correct the
cluster size p-value based on DOF (degree of freedom), like the t-ratios
table including a DOF? Thanks a lot!
Best regards,
Ting
On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Correct. This is no different than, eg, a t-test. Look in the back of a
> stats book from the 1950s and you will find a table of t-ratios and
> corresponding p-values. Obviously, they did not have access to any of the
> data being analyzed today:), but the tables are still valid.
>
> On 12/2/2019 2:03 PM, Ting Li wrote:
>
> External Email - Use Caution
> 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. <
> dgr...@mgh.harvard.edu> wrote:
>
>>
>>
>> On 12/2/2019 11:58 AM, Ting Li wrote:
>>
>> 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 ?
>>
>> 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. <
>> dgr...@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 Caution
>>> 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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