Re: [Freesurfer] Multiple comparison using Monte Carlo
External Email - Use Caution Dear Dr. Douglas, Thank you so much! Best regards, Ting On Thu, Dec 5, 2019 at 11:45 AM Greve, Douglas N.,Ph.D. < dgr...@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. > > mailto: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. > >> mailto: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. > >>> mailto: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). > >>>
Re: [Freesurfer] Multiple comparison using Monte Carlo
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
Re: [Freesurfer] Multiple comparison using Monte Carlo
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.
mailto: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.
mailto: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.
mailto: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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Re: [Freesurfer] Multiple comparison using Monte Carlo
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
>>>
>>> ___
>>> Freesurfer mailing
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing
>>
Re: [Freesurfer] Multiple comparison using Monte Carlo
External Email - Use Caution
Dear Dr. Douglas,
Thank you so much for your explanation. You really helped me 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
>>>
>>> ___
>>> Freesurfer mailing
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Re: [Freesurfer] Multiple comparison using Monte Carlo
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.
mailto: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.
mailto: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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Re: [Freesurfer] Multiple comparison using Monte Carlo
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
>>
>> ___
>> Freesurfer mailing
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Multiple comparison using Monte Carlo
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.
mailto: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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Multiple comparison using Monte Carlo
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. <
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
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Multiple comparison using Monte Carlo
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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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Multiple comparison using Monte Carlo
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___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
