on-orthogonal design matrices wrong
>>>> or is it allowed to do this instead of using tools like palm (what
>>>> happens eg with the covariates when using forced permutation)? I
>>>> used forced permutation and it seemed to work, results were (partly)
>>>
t appropriate. Check the winkler paper, I
> >>> think he talks about what happens if you just don't do anything.
> >>>
> >>>
> >>> On 08/29/2016 11:07 AM, maaike rive wrote:
> >>>> Hi all,
> >>>>
> >>>>
permutation for non-orthogonal design matrices wrong
>>>> or is it allowed to do this instead of using tools like palm (what
>>>> happens eg with the covariates when using forced permutation)? I
>>>> used forced permutation and it seemed to work, results were (p
enter for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave.Tel: 314-747-6173
>>> St. Louis, MO 63110Email: mha...@wustl.edu
>>>
>>> From: >> <
n using forced permutation)? I
>>> used forced permutation and it seemed to work, results were (partly)
>>> comparable to what I found with monte carlo simulations.
>>>
>>>
>>> Thanks, Maaike
>>>
>>>
>>>
>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
>> namens Harms, Michael
>>
>> *Verzonden:* vrijdag 26 augustus 2016 01:00:13
>> *Aan:* Freesurfer support list
>> *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing
>> running aft
;>
> Date: Thursday, August 25, 2016 at 4:13 PM
> To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running
> after 3 days!
>
> Hi Doug,
>Thanks for the help! I think I figured
o:freesurfer@nmr.mgh.harvard.edu>>
> Date: Thursday, August 25, 2016 at 4:13 PM
> To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] mri_glmfit-sim permutation testing running
> after 3 days!
>
> Hi Doug,
>T
f Ajay Kurani
mailto:dr.ajay.kur...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, August 25, 2016 at 4:13 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mri_glmfit-sim permutati
gt; on behalf of Ajay Kurani <dr.ajay.kur...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, August 25, 2016 at 4:13 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit-sim permutation
On 08/25/2016 05:13 PM, Ajay Kurani wrote:
> Hi Doug,
>Thanks for the help! I think I figured out the issue based on your
> response.
> 1) I created a template to use for this group and named it fsaverage
> (including creating monte carlo simulations) for simplicity of
> integrating with
Hi Doug,
Thanks for the help! I think I figured out the issue based on your
response.
1) I created a template to use for this group and named it fsaverage
(including creating monte carlo simulations) for simplicity of integrating
with freesurfer as I am newer to it. This is why the sizes didn'
Something strange is going on in your data. You are using fsaverage, but
the size of the data in PDvsMCI_lh_thickness_10mm/y.mgh does not match
(it has 148278 vertices, not 163842 of fsaverage). This is causing the
processes to die, but the backgrounding software does not know that the
process
Can you tar up the glmdir and drop it to me at our filedrop (link
below)? Also,what version of FS are you using? Also, can you try running
it without backgrounding on a few (say, 100) iterations to see if it
completes? Then try with backgrounding (problem may be backgrounding)
On 08/25/2016 01
Hi Freesurfer Experts,
I am trying to use freesurfer's mri_glmfit-sim tool to run permutation
testing on cortical thickness data (as recommended by Doug in my previous
post:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg48653.html )
Most of the tutorials I found were not relat
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