On Thu, Dec 5, 2019 at 11:45 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

I've attached a couple of papers

On 12/3/19 9:24 PM, Ting Li wrote:
>
>         External Email - Use Caution
>
> Dear Dr. Douglas,
>
> Thank you so much.
>
> I have difficulty to understand z map is essentially an infinite # of
> subjects.
> Before smooth, there is no GLM analysis. Does the smooth include in
> the GLM process?
>
> Best regards,
> Ting
>
> On Tue, Dec 3, 2019 at 2:14 PM Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>
>
>
> On 12/3/2019 1:36 PM, Ting Li wrote:
>>
>>          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?)
>>
> The Z is essentailly an infinite # of subjects (it is just a
> single map).
>>
>> * 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? )
>>
> The GLM analysis, from the residual.
>>
>> * threshold z map (Does it mean a GLM analysis so we can have
>> threshold z map?)
>>
> No, the z-map is synthesized directly
>
> The simulation is done in mri_glmfit-sim and in mri_mcsim.
>
>> 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!
> I don't know what you mean.
>>
>> Best regards,
>> Ting
>>
>> On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D.
>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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.
>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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).
>>>>
>>>> ClusterwiseCorrection for Multiple Comparisons
>>>> To perform a cluster-wise correction for multiple
>>>> comparisons, we will run a simulation. The simulation
>>>> isa way to get a measure of the distribution of the
>>>> maximum cluster size under the _null __hypothesis_.
>>>> This isdone 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
>>>> <mailto: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 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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