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. <
dgr...@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. <
> 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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