Yes, 3 is p<.001, which is converted to a z before thresholding the map.
Note that we are trying to push people to use permutation instead of MC.
On 07/09/2018 05:22 PM, Dincer, Aylin wrote:
>
>
> Hi FreeSurfer experts,
>
>
> I am trying to understand the Monte Carlo Z simulation in FreeSufer
>
External Email - Use Caution
Hi FreeSurfer experts,
I am trying to understand the Monte Carlo Z simulation in FreeSufer
(mri_glmfit-sim) and have a question about the vertex wise /cluster forming
threshold.
In the simulation, a vertex wise threshold (ex. -cache 3 abs) is set
arch 12, 2015 10:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Simulation
>
> Yes, that probably is the reason.
> doug
>
> On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote:
>> To be honest, I checked the between subject alignment and it look
...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, March 12, 2015 10:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation
Yes, that probably is the reason.
doug
On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote:
>
t; From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, March 12, 2015 2:47 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Simulation
>
> I meant whi
: Thursday, March 12, 2015 2:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation
I meant which ones are causing the problems when you run mri_glmfit.
When you run fslview you will see something that looks like a brain. As
you scroll thru the different time points
to do the first level
>> analysis for fct. connectivity instead of PASL for example?
>>
>> Thanks,
>> Rick
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of D
half of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, March 12, 2015 12:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation
If the registration looks ok, then that is all that counts. However, I'm
a bit sceptical that the reg looks ok but
vard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, March 11, 2015 6:34 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Simulation
>
> For the range, lower is better,
reesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, March 11, 2015 5:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Simulation
>
> Try checking the individual registrat
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, March 11, 2015 3:22 PM
> To: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Simulation
&
nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, March 11, 2015 5:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Simulation
>
> Try checking the individual registrations (or look at the first value
eps to simplify the script a little bit.
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, March 11, 2015 4:50 PM
> To: freesurfer@nmr.mgh.harva
ittle bit.
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, March 11, 2015 4:50 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carl
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, March 11, 2015 4:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation
I still can't really tell what it is doing. It looks like it is
reesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Simulation
>
> Sorry, I don't have time to deconstruct that script. Can you simplify it
> for me?
>
> On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
>> This is the script I am using to
, 2015 3:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation
Sorry, I don't have time to deconstruct that script. Can you simplify it
for me?
On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote:
> This is the script I am using to create cbf.talar
, 2015 3:22 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Monte Carlo Simulation
Something went very wrong with your first level analysis because the
final mask is pretty messed up. how did you create cbf.talairach.mgz ?
On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote
Something went very wrong with your first level analysis because the
final mask is pretty messed up. how did you create cbf.talairach.mgz ?
On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote:
> Hi Doug et al.,
>
> Here is the glmdir file you were requesting:
> http://gate.nmr.mgh.harvar
Hi Doug et al.,
Here is the glmdir file you were requesting:
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928
Thanks,
Rick
From: Wolthusen, Rick Peter Fritz
Sent: Tuesday, March 10, 2015 2:10 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: RE: Mon
mris_preproc might work. You could also use mri_concat (mris_preproc is
a front end for mri_concat)
On 03/03/2015 06:19 PM, Janosch Linkersdörfer wrote:
>
> Am 03.03.2015 um 14:42 schrieb Douglas N Greve :
>
>> Some of this Martin will have to comment on, but my comments below
>>
>> On 03/03/201
Am 03.03.2015 um 14:42 schrieb Douglas N Greve :
>
> Some of this Martin will have to comment on, but my comments below
>
> On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote:
>> Hey Doug,
>>
>> thanks again! That means, I would do something like:
>>
>> 1.) construct longitudinal qdec table
Some of this Martin will have to comment on, but my comments below
On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote:
> Hey Doug,
>
> thanks again! That means, I would do something like:
>
> 1.) construct longitudinal qdec table
> - only use fsid, fsid-base, and years/age columns
> - substract
Hey Doug,
thanks again! That means, I would do something like:
1.) construct longitudinal qdec table
- only use fsid, fsid-base, and years/age columns
- substract the average age of the one-time point subjects from years/age value
for every subject at every time point
2.) run long_mris_slopes
-
I don't know, esp since it is an approximation to begin with. An
alternative is to take the offsets from your multi-time-point subjects
and the single maps from your subjects with one time point and run that
through the one-sample-group-mean (--osgm in mri_glmfit). If you go this
route, then y
Hi Doug,
thank you very much for your answer!
Am 02.03.2015 um 11:30 schrieb Douglas N Greve :
>
> You would do the long analysis using a random effects analysis.
OK, so basically do 2-stage modeling
(https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right?
> For each sub
Hi Rick, in the future please post to the list and not to us personally.
Thanks! When you did the volume-based analysis, it should have masked
out anything anything that was not subcortical. Did it not? If not, then
when you run mri_glmfit you can add --mask
$SUBJECTS_DIR/fsaverage/mri.2mm/bra
You would do the long analysis using a random effects analysis. For each
subject you can get a slope (this won't work if the subject only has 1
time point), then concatenate the slopes into a file and run mri_glmfit,
then follow the procedures from the archive email you reference.
doug
On 02/2
Hi Doug and others,
I would like apply (Monte Carlo simulation) cluster correction (as opposed to
the implemented vertex-wise FDR correction) on the results from a longitudinal
study I analyzed using the LME toolbox. The design is unbalanced (different
number of time points, from 1 to 4, per su
Thanks, Doug!
I looked at the examples on the wiki, and the Paired Analysis wiki page as well.
You mentioned I should include the categorical and continuous variables in the
fsgd file for the mri_glmfit. It seems that one of my analyses includes few
subjects, and then one of the class end up lac
On 04/15/2014 10:34 PM, Pedro Rosa wrote:
> Hi, Doug.
> Thanks a lot!
> The command would look like this: mri_glmfit-sim --glmdir
> lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs
> --overwrite --cache 1.3 abs
> It takes only a few seconds to run.
The command is fine, but remove
Hi, Doug.
Thanks a lot!
The command would look like this: mri_glmfit-sim --glmdir
lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs --overwrite
--cache 1.3 abs
It takes only a few seconds to run.
I have a few questions about how to run it:
1) How the single entry for each subject
On 04/14/2014 10:35 AM, Pedro Rosa wrote:
> Dear Doug and Jorge,
> I tried what you suggested and I think it work, although I have some
> concerns.
> I am working with a longitudinal study with two time-points for all
> subjects, three categorical variables (group, substance abuse /
> dependenc
Dear Doug and Jorge,
I tried what you suggested and I think it work, although I have some concerns.I am working with a longitudinal study with two time-points for all subjects, three categorical variables (group, substance abuse / dependence and
Thanks, Doug!
Should I run the mri_preproc and and smooth the output using mri_surf2surf
with, let’s say, 10mm, and than run the LME normally in MatLab?
Would this be problematic with a different smoothing procedure in mri_glmfit?
How will mri_glmfit deal with the longitudinal design? Does this
I think I would just run mri_glmfit on your data to get the proper
directly structure and estimate of FWHM, then copy the sig file from the
mixed fx analysis into the glmfit folder for one of the contrasts. Then
run mri_glmfit-sim.
doug
On 3/29/14 10:29 AM, Pedro Rosa wrote:
Dear Doug and
Dear Doug and Jorge,
Thank you very much for your help.
I found another message in the list
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html)
in which you suggested a way of using MC in mri_glmfit-sim by creating “fake
files”, which would not be read by the scrip
Jorge, do you output the FWHM?
doug
On 03/27/2014 03:14 PM, jorge luis wrote:
> Hi Pedro
>
> Sorry, right now the only multiple comparisons corrections implemented
> in lme are the original Benjamini and Hochberg (1995) FDR procedure
> (lme_mass_FDR) and a more recent and powerful two-stage FDR
Hi Pedro
Sorry, right now the only multiple comparisons corrections implemented in lme
are the original Benjamini and Hochberg (1995) FDR procedure (lme_mass_FDR) and
a more recent and powerful two-stage FDR procedure (lme_mass_FDR2):
Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive
Dear Doug,
Thank you very much!
I will try what you suggested, although I am not sure if Jorge's stream
outputs the FMHM, or if I would need to run the statistics from the beggining
using in the terminal, and not in MatLab.
Do you think Jorge could comment on this issue?
Regards,
Pedro Rosa.
On
In theory, it should be possible. I have not used Jorge's stream, so I
don't know that much about it. Does it save an estimate of the FWHM? If
so, then you can run mri_surfcluster passing it the p-value (ie,
-log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. This is
what mri_glmfi
Dear list,
I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline in a
structural MRI dataset and I would like to use Monte Carlo as the method for
correction for multiple comparisons. However, the longitudinal LME tutorial
includes only FDR correction (lme_mass_FDR2).
Is it possible
All vertices in the cluster will have this value. It can be found in the
"summary" file in each contrast. It is the final clusterwise p-value,
ie, the probability of seeing a cluster of the given size by random chance.
doug
On 01/28/2014 05:07 PM, Natasha Haris wrote:
> Where does it appear
QDEC computes it
On 01/28/2014 04:52 PM, Natasha Haris wrote:
> And does the monte carlo precomputed simulation data in the QDEC GUI
> compute this final p-value? Or do I need to use any commands namely
> mri_glmfit?
>
>
> On Tue, Jan 28, 2014 at 1:38 PM, Douglas N Greve
> mailto:gr...@nmr.mg
The cluster-forming threshold is needed to define what the clusters are.
Once you have a cluster forming threshold, you get clusters with a
certain size. Given the size, the FWHM, the cluster forming threshold,
and the search space, a p-value for the cluster is computed.
On 01/28/2014 03:58 PM
So sorry for all the beginner questions. One more.
Then what is the point of running the Monte Carlo simulation with a
cluster-forming threshold of p<0.01 or any other threshold for that matter if I
already know what the clusterwise threshold min should be?
Natasha
> On Jan 28, 2014, at 1
Yes
On 01/28/2014 03:35 PM, Natasha Haris wrote:
> So then how does one determine what should go into the Threshold min
> box? (If it's usually p<0.05 should the clusterwise corrected
> Threshold min be 1.3?)
>
> Natasha
>
>
> On Tue, Jan 28, 2014 at 12:30 PM, Douglas N Greve
> mailto:gr...@n
So then how does one determine what should go into the Threshold min box?
(If it's usually p<0.05 should the clusterwise corrected Threshold min be
1.3?)
Natasha
On Tue, Jan 28, 2014 at 12:30 PM, Douglas N Greve wrote:
>
> On 01/28/2014 03:26 PM, Natasha Haris wrote:
>
>> Oops sorry!
>>
>> I g
On 01/28/2014 03:26 PM, Natasha Haris wrote:
> Oops sorry!
>
> I guess my question then is, after running the monte carlo simulation
> with this cluster-forming threshold (p<0.01), is there a specific
> corrected (clusterwise) threshold I can/am supposed to place in the
> Threshold min box? Or
Oops sorry!
I guess my question then is, after running the monte carlo simulation with
this cluster-forming threshold (p<0.01), is there a specific corrected
(clusterwise) threshold I can/am supposed to place in the Threshold min
box? Or are these two not related in any way.
Natasha
On Tue, Jan
Hi Natasha, please remember to post to the list! When you say a
different set of blobs, do you mean that none of the original blobs are
there? Or do some of the blobs just disappear? Note that the threshold
you use in the simulation is not related to the "Threshold Min". In this
case, the Thre
Yes, when looking at the corrected images, the Threshold Min because the
clusterwise threshold. So if you want to see only clusters that have a
clusterwise p<.05, set that threshold to 1.3
doug
On 01/28/2014 02:24 PM, Natasha Haris wrote:
> The clusterwise simulation runs with a p<0.05 thr
On 01/24/2014 11:54 AM, Natasha Haris wrote:
> Dear Freesurfers,
>
> I am slightly confused about the monte carlo simulation.
>
> First off, I only find a blob when I run the p<0.05 threshold level and don't
> see anything else when I run simulations with p less than that. What does
> this mean?
Dear Freesurfers,
I am slightly confused about the monte carlo simulation.
First off, I only find a blob when I run the p<0.05 threshold level and don't
see anything else when I run simulations with p less than that. What does this
mean?
Additionally, when I click on any question of interest
rvard.edu
> Sent: Wednesday, September 4, 2013 10:36:14 AM
> Subject: Re: [Freesurfer] Monte Carlo Simulation in Qdec
>
>
> Hi Tara,
> You can try with fwhm=0 as Doug suggested, or 5 if it works. I'm still trying
> to see whether the level of fwhm could be modified in qdec
k Schmansky" , freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, September 4, 2013 10:36:14 AM
Subject: Re: [Freesurfer] Monte Carlo Simulation in Qdec
Hi Tara,
You can try with fwhm=0 as Doug suggested, or 5 if it works. I'm still trying
to see whether the level of fwhm could be modified in q
Hi Tara,
You can try with fwhm=0 as Doug suggested, or 5 if it works. I'm still trying
to see whether the level of fwhm could be modified in qdec so that you can
input your own level (e.g. 1 or 2, instead of the specified 0-5-10-15-20-25).
Nick,
Do you know if there is a keyword that can be cha
Hi Tara, The problem is that the lGI is already very smooth and then it
gets smoothed again. This causes the total smoothness level to go beyond
what has been done for the simulation. Try using fwhm=0.
doug
On 09/04/2013 09:48 AM, Tara Ann Miskovich wrote:
> Hello,
>
> I am conducting group a
Hello,
I am conducting group analyses with LGI data in qdec, and I am having an issue
with the monte carlo simulation I am hoping to get help with.
Under design I leave the Smoothing (FWHM) at 10, and when I try to run the
monte carlo simulation after running the analysis I get this error: Err
>>>>>>> 1.86776 1.0 -0.00010 1.0
>>>>>>>>> 125 4 32.0 64.00 23.00 76.00
>>>>>>>>> 1.86629 1.0 -0.00010 1.0
>>>>>>>>> 126
;>>> 1.81496 1.0 -0.00010 1.0
>>>>>>> 135 2 16.0 9.007.00 43.00
>>>>>>> 1.80712 1.0 -0.00010 1.0
>>>>>>> 136 1 8.0 36.002.00 53.00
>&g
t;> 1.79309 1.0 -0.00010 1.0
>>>>>> 142 4 32.0 61.00 43.00 84.00
>>>>>> 1.78916 1.0 -0.00010 1.0
>>>>>> 143 1 8.0 13.00 13.00 34.00
>>&
t;>>>> 148 1 8.0 24.001.00 50.00 1.77625
>>>>> 1.0 -0.00010 1.0
>>>>> 149 1 8.0 3.00 35.00 84.00 1.77073
>>>>> 1.0 -0.00010 1.0
>>
28.00 67.00 70.00 1.74531
>>> 1.0 -0.00010 1.0
>>> 163 1 8.0 4.00 33.00 30.00 1.74303
>>> 1.0 -0.00010 1.0
>>> 164 1 8.0 69.00 20.00 74.00
3
>> 1.0 -0.00010 1.0
>> 171 1 8.0 25.00 65.00 86.00 1.72933
>> 1.0 -0.00010 1.0
>> 172 1 8.0 40.00 10.00 56.00 1.72897
>> 1.0 -0.00010 1.0
>>
00010 1.0
> 181 1 8.0 51.007.00 19.00 1.70870
> 1.0 -0.00010 1.0
> 182 1 8.0 43.001.00 48.00 1.70621
> 1.0 -0.00010 1.0
> 183 1 8.0 22.00 36.00 41.00
1.0
Date: Tue, 25 Jun 2013 12:22:23 -0400
From: Douglas N Greve
Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach
coordinates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <51c9c3bf.7000...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=
can you send the file?
On 06/25/2013 10:08 AM, Emily Boeke wrote:
> Hi All,
>
> I'm running Monte Carlo simulations on functional data, and the coordinate
> information outputted in the cluster.summary file isn't making sense. Usually
> the coordinates for the clusters listed are Talairach coord
Hi All,
I'm running Monte Carlo simulations on functional data, and the coordinate
information outputted in the cluster.summary file isn't making sense. Usually
the coordinates for the clusters listed are Talairach coordinates, but in the
.summary files I'm getting, the coordinates are labeled
On 06/05/2013 10:17 AM, std...@virgilio.it wrote:
> Hi list,
>
> I performed Monte Carlo simulation on my cortical thickness analysis.
> Now, I have significant clusters in the map for p<0.05. Is possible to
> obstain form each significant cluster the real value of p?
>
> Thanks,
>
>
> Stefano
>
>
what do you mean by the real value of p?
On 6/5/13 10:17 AM, std...@virgilio.it wrote:
Hi list,
I performed Monte Carlo simulation on my cortical thickness analysis.
Now, I have significant clusters in the map for p<0.05. Is possible to
obstain form each significant cluster the real value of
Hi list,
I performed Monte Carlo simulation on my cortical thickness analysis. Now, I
have significant clusters in the map for p<0.05. Is possible to obstain form
each significant cluster the real value of p?
Thanks,
Stefano ___
Freesurfer mailing li
our help
> Regards
> Koushik
>
>
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 15, 2012 10:41 AM
> To: Govindarajan, Koushik Athreya
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] monte carlo simulation question
>
> In pr
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 15, 2012 10:41 AM
To: Govindarajan, Koushik Athreya
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] monte carlo simulation question
In principal, it should be the same
AM
> To: Govindarajan, Koushik Athreya
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] monte carlo simulation question
>
> Hi Koushik, download this file and copy it into the mri/transforms directory
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talaira
: [Freesurfer] monte carlo simulation question
Hi Koushik, download this file and copy it into the mri/transforms directory
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.xfm
Then rerun mri_glmfit-sim with the --no-sim option so that it picks up
where it left off. You will need to give
Hi Koushik, download this file and copy it into the mri/transforms directory
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/talairach.xfm
Then rerun mri_glmfit-sim with the --no-sim option so that it picks up
where it left off. You will need to give the "csdbase" which you passed
i
Hello group,
I am running the multiple comparisons simulation after my mri_glmfit
finished. I see that it went through all the iterations and then quit with the
following error message it could not find the talairach.xfm file in my average
brain. I did not use the fsaverage and instead
Hi Alex, try reading these papers:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hayasaka.2003.ni.1014.clustersize.pdf
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/hagler.2006.ni.surfcluster.pdf
if you still have questions, feel free to ask.
doug
Alexander Ivano
*Dear Freesurfer Users and Developers,
*
Could you please help me to clarify the key steps implemented into the
Monte Carlo approach for multiple comparisons correction? As far as I
understood, it consists of running many permutations for fitting the
measurements of different ROI sizes, which are b
Have you looked at mri_glmfit-sim --help yet?
doug
Prapti Gautam wrote:
Dear Freesurfers,
I ran a monte carlo simulation for thickness analyses using mri_glmfit
and found new files in the contrast subdirectory. I was able to figure
out what the first two represent, but was wondering if a
Dear Freesurfers,
I ran a monte carlo simulation for thickness analyses using mri_glmfit
and found new files in the contrast subdirectory. I was able to figure
out what the first two represent, but was wondering if any one could
clarify what information the rest of the files show:
mc-z.nega
Zhangyuanchao
Sent: Tuesday, November 04, 2008 9:20 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Monte carlo simulation for multiple comparison on
asurface
Dear Mr or Ms,
How can I do Monte carlo simulation for multiple comparison correction on a
surface. which command should I
Dear Mr or Ms,
How can I do Monte carlo simulation for multiple comparison correction on a
surface. which command should I launch?
I also want to know about permutation test.
could you tell me how to use them?
yczhang
-
雅虎邮箱，您的终生邮箱！
Dear Mr or Ms,
How can I do Monte carlo simulation for multiple comparison correction?
I also want to know about permutation test.
could you tell me how to use them?
yczhang
-
雅虎邮箱，您的终生邮箱！___
Freesurfer ma
Actually, I do have the fwhm.dat file...
I was just commenting on how obvious that should have been to me!
Thanks, though!
- Jerry
On Fri, Apr 18, 2008 at 10:56 AM, Pratap Kunwar <[EMAIL PROTECTED]>
wrote:
> Jerry,
>
> can you post your command lines and log file? there should be fwhm.dat
> along
Jerry,
can you post your command lines and log file? there should be fwhm.dat
along with the y.fsgd.
> How did I miss that???
> Thanks!
> - Jerry
>
> On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve <[EMAIL PROTECTED]>
> wrote:
>
>> there should be a fwhm.dat file in the output.
>>
>> doug
>>
>>
>> J
How did I miss that???
Thanks!
- Jerry
On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve <[EMAIL PROTECTED]>
wrote:
> there should be a fwhm.dat file in the output.
>
> doug
>
>
> Jerry Yeou-Wei Chen wrote:
>
> Hello,
>
> I have a question regarding performing Monte Carlo simulations when a
> custom d
there should be a fwhm.dat file in the output.
doug
Jerry Yeou-Wei Chen wrote:
Hello,
I have a question regarding performing Monte Carlo simulations when a
custom design matrix is being used.
The wiki says that "For both MC simulations, you must supply the
smoothness of your data as Full-Wi
Hello,
I have a question regarding performing Monte Carlo simulations when a custom
design matrix is being used.
The wiki says that "For both MC simulations, you must supply the smoothness
of your data as Full-Width/Half-Max (FWHM) of the residual. This can be
obtained from the ResidualFWHM value
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