External Email - Use Caution
Hi Freesurfer experts,
I'm very sorry to bother you, but I am very confused with the
following questions:
My experimental design includes two discrete factors:
with three levels (d,m,h); gender (f, m), and two Nvariables
So I can
Do you mean the difference between the d,m,h classes? If so, it would be
1 1 -1 -1 0 0 (rest all 0s)
1 1 0 0 -1 -1 ...
0 0 1 1 -1 -1 ...
On 4/14/2022 9:50 AM, David wrote:
External Email - Use Caution
Hi Freesurfer experts,
I'm very sorry to bother you, but I am very confused
External Email - Use Caution
Hi Freesurfer experts,
I'm very sorry to bother you, but I am very confused with the
following questions:
My experimental design includes two discrete factors:
with three levels (d,m,h); gender (f, m), and two Nvariables
So I can
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
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
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 s
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
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
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 P
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
On 12/2/2019 11:58 AM, Ting Li wrote:
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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 he
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 me
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:
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Dear Freesurfer Expert:
I have used the simulation code as show below:
mri_glmfit-sim \
--glmdir lh.gende
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
speci
Have you seen this tutorial?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
it uses permutation (which does not work with weighted least squares),
but you could change it to use the old monte carlo stuff.
On 7/29/19 2:15 PM, FAST Study wrote:
>
> Externa
See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm?highlight=%28permutation%29
On 07/16/2018 02:15 PM, Ting Li wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> I just try your suggestion. It gives me information like the
> following. What does
External Email - Use Caution
Hi Douglas,
I just try your suggestion. It gives me information like the following. What
does the design matrix stands for? Thanks.
Ting
ERROR: design matrix is not orthogonal, cannot be used with permutation.
If this something you really want to d
My guess is that something is going wrong with the backgrounding. Try
running it without the --bg option. You can run it with a few (eg, 100)
iterations just to see if it finishes.
On 07/05/2018 12:34 PM, Ting Li wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
>
>
Hello, I want to run a whole brain cortical thickness analysis and I will like to confirm some steps. a) for correcting for multiple comparison, I want to use both Monte Carlo and permutations in order to compare the difference. Are these the right commands? Monte Carlo : mri_glmfit-sim --glmdir
Thank you, Anderson.
Regards.
VM
On Thu, Feb 2, 2017 at 11:06 PM, Anderson M. Winkler wrote:
> Hi VM,
>
> They can stay all in the same .csv file. The "fwep" files will have
> p-values corrected across all columns of this input.
>
> All the best,
>
> Anderson
>
>
> On 2 February 2017 at 12:09,
Hi VM,
They can stay all in the same .csv file. The "fwep" files will have
p-values corrected across all columns of this input.
All the best,
Anderson
On 2 February 2017 at 12:09, neuroimage analyst <
neuroimage.anal...@gmail.com> wrote:
> Thanks, Anderson. If there are several other measures
Hi,
We extracted volume measures from 7 ROIs in 2 groups and compared
a) Mean of each ROI volume between group, and compared independently such
as
i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2
ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2
and so
Thanks, Anderson. If there are several other measures such as volume,
thickness, FA, can I then put them in a single csv file and run the
command or I have to create 3 csv files, one each for volume, thickness,and
FA and also invoke -corrmod?
Thanks
Regards
VM
On Feb 2, 2017 1:01 AM, "Anderson
Hi VM,
Please see below:
On 1 February 2017 at 02:38, neuroimage analyst <
neuroimage.anal...@gmail.com> wrote:
> Hi,
>
> We extracted volume measures from 7 ROIs in 2 groups and compared
> a) Mean of each ROI volume between group, and compared independently such
> as
> i) whether mean of ROI 1
I would say yes, but I've seen plenty of pubs that do not correct. The
bonferroni correction is fine. You could also try FDR (though on 4
points it might not make much sense).
On 01/10/2017 01:47 PM, neuroimage analyst wrote:
> Hi,
>
> I extracted thalamic, caudate, and putamen volume (left hem
Hi,
I extracted thalamic, caudate, and putamen volume (left hemisphere), and
cingulate thickness (right hemisphere) from freesurfer's parcellation. Then
I compare these volumes and thickness across two groups using R and found
significant differences in these measurements. Do I have to correct for
On 10/17/16 2:16 AM, Ajay Kurani wrote:
Hi Doug,
I had some additional questions regarding multiple comparisons in
Freesurfer.
1) Do you correct the left and right hemispheres separately or combine
both together for muliple comparison correction?
We correct each hemi independently and the
Hi Doug,
I had some additional questions regarding multiple comparisons in
Freesurfer.
1) Do you correct the left and right hemispheres separately or combine both
together for muliple comparison correction?
2) Say you are testing multiple contrasts in your model: A > B, A< B etc.
Do you correct
On 8/3/16 3:45 AM, Ajay Kurani wrote:
Hi Doug,
Thank you very much for your update regarding this issue.
1)Just curious, will LGI be included in this report as this is another
analysis of interest?
I was not planning to. The 809 subjects that I used for thickness do not
have lGI run on th
Hi Doug,
Thank you very much for your update regarding this issue.
1)Just curious, will LGI be included in this report as this is another
analysis of interest?
2)As for the cortical thickness I originally used 15mm in the analysis so
based on your email I think using 5-10mm may be more prudent
I have been doing simulations similar to #1 (Eklund) using
surface-based analysis on both thickness and fMRI. I'll prepare a report
of the results, but the early indications are that the same effect is in
play, though it does not look like the effects are as bad as in Eklund.
For thickness ana
Hello Freesurfer Experts,
Recently there were two article published regarding clusterwise
simulations for volumetric fmri analyses and potential errors for
underestimating clusterwise extent thresholds.
1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes
2) biorxiv.org/content/early
Hi,
I have performed a linear mixed model analysis on surface data in AFNI using
SUMA, resulting in each vertex having a p value. I would like to perform a
multiple comparison correction using freesurfer, as an FDR approach in AFNI
is to stringent (individual vertex statistical thresholds are low)
Hi Freesurfers,
More questions about this analysis.
1) Referring to the documentation, we used the following command:
tksurfer fsaverage lh inflated -annot mc-z.abs.2.sig.ocn.annot -fthresh 2
-curv -gray
The documentation says we should see an image as shown in Figure 1
(attached). But what we s
The dsign.con looks something like this:
--cut here ---
%! VEST-Waveform File
/NumWaves 2
/NumContrasts 2
/PPheights 1.00e+00 1.00e+00
/Matrix
1.00e+00 -1.00e+00
-1.00e+00 1.00e+00
- cut here -
Hi Doug, we are eager to try the FSL randomise program on a FS data set we
have. However, we have one (stupid, maybe) question: is the file
design.con something that we make manually, or is it generated by some of
the previous processes?
If we are going to make it ourselves, how should it be?
In o
FYI, FSL has a nice site documenting the randomise program :)
http://www.fmrib.ox.ac.uk/fsl/randomise/index.html
Doug Greve wrote:
mris_glm does not correct for multiple comparisons itself. However,
you can use fdr inside of tksurfer, or ...
Steve Smith and I just worked out how to use t
mris_glm does not correct for multiple comparisons itself. However, you
can use fdr inside of tksurfer, or ...
Steve Smith and I just worked out how to use the FSL randomise program
to compute the vertex-wise threshold. Randomise implements permutation
testing, which is much less conservativ
Hi,
I am running mris_glm to compare the cortical thickness between two groups.
I have a question, which method is used for correcting multiple comparison
in the analysis? Thanks,
Antao
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