Re: [Freesurfer] Multiple comparison - permutation

[Douglas N. Greve]

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 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 do, run with --perm-force
>> On Jul 16, 2018, at 1:09 PM, Douglas N. Greve > > wrote:
>>
>>
>> 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,
>>>
>>> I am running the multiple comparison (permutation) on a MAC with the
>>> following code. It has taken 8 hours and has not finished yet. It
>>> gives me Poll jobs information without end. According to tutorial
>>> information, it will only take around 20 minutes. Do you know what
>>> should I do if I want to use this perm multiple comparison? I have
>>> attached my MAC system information and the Poll jobs information.
>>> Thanks a lot!
>>>
>>> Best wishes,
>>> Ting
>>>
>>> mri_glmfit-sim \
 --glmdir lh.volume_70_sTIV_perm.glmdir \
 --perm 1000 4.0 neg \
 --cwp 0.05\
 --2spaces \
 --bg 2
>>>
>>>
>>>
>>>
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>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>>
>>
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>> and properly
>> dispose of the e-mail.
>
>
>
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Re: [Freesurfer] Multiple comparison - permutation

[Ting Li]

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 do, run with --perm-force
> On Jul 16, 2018, at 1:09 PM, Douglas N. Greve  wrote:
> 
> 
> 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,
>> 
>> I am running the multiple comparison (permutation) on a MAC with the 
>> following code. It has taken 8 hours and has not finished yet. It 
>> gives me Poll jobs information without end. According to tutorial 
>> information, it will only take around 20 minutes. Do you know what 
>> should I do if I want to use this perm multiple comparison? I have 
>> attached my MAC system information and the Poll jobs information. 
>> Thanks a lot!
>> 
>> Best wishes,
>> Ting
>> 
>> mri_glmfit-sim \
>>>   --glmdir lh.volume_70_sTIV_perm.glmdir \
>>>   --perm 1000 4.0 neg \
>>>   --cwp  0.05\
>>>   --2spaces \
>>>   --bg 2
>> 
>> 
>> 
>> 
>> ___
>> 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 
> 
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline 
>  . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Multiple comparison - permutation

[Douglas N. Greve]

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,
>
> I am running the multiple comparison (permutation) on a MAC with the 
> following code. It has taken 8 hours and has not finished yet. It 
> gives me Poll jobs information without end. According to tutorial 
> information, it will only take around 20 minutes. Do you know what 
> should I do if I want to use this perm multiple comparison? I have 
> attached my MAC system information and the Poll jobs information. 
> Thanks a lot!
>
> Best wishes,
> Ting
>
> mri_glmfit-sim \
> >   --glmdir lh.volume_70_sTIV_perm.glmdir \
> >   --perm 1000 4.0 neg \
> >   --cwp  0.05\
> >   --2spaces \
> >   --bg 2
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.