Re: [Freesurfer] correlation coefficient R

[tom parker]

Thank you so much Doug!

It worked! I was just wondering which value I should report as the
correlation coefficient of my analysis.

This is the output I got:

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
  1  -4 2037320373.0  Seg-004-0.1596 0.0468-0.3134
-0.1017 0.2117

Should I report the mean (-0.1596) or the min (-0.3134)?

Thanks again

Try something like

mri_segstats --i pcc.mgh --seg cluster.ocn.mgh --excludeid 0 --sum
cluster.pcc.dat



2017-04-08 1:35 GMT+01:00 tom parker :

> Hi Doug,
>
> Thank you for your answer!
>
> It would be great if you could send me some instructions.
>
> Thanks for the help!
>
> Douglas N Greve
> 
>  Thu,
> 06 Apr 2017 13:32:07 -0700
> 
>
> I guess you could average it over space (eg, over a cluster). Let me
> know if you want instructions. Otherwise, I'm not sure what to say.
>
>
>
> 2017-04-04 11:49 GMT+01:00 tom parker :
>
>> Hi Doug,
>>
>> Thanks! I realize now I didn't explain myself properly.
>>
>> I need one single R value for the correlation analysis I made, similarly to 
>> when I correlate two variables with Pearson's R in a statistical package.
>>
>> I have a referee asking me to put it on a table with the freesurfer results. 
>> Is there a way to get a single average R value from the pcc.mgh file?
>>
>> Thank you so much!
>>
>>
>> Douglas Greve
>> 
>>  Mon,
>> 03 Apr 2017 18:46:46 -0700
>> 
>> Each vertex is a correlation value.
>>
>>
>>
>> 2017-04-04 1:09 GMT+01:00 tom parker :
>>
>>> Thanks Doug!
>>>
>>> I have version 6 and got a pcc.mgh file.
>>>
>>> How can I get a correlation R value from this file?
>>>
>>> Thanks again
>>>
>>> Douglas N Greve
>>> 
>>>  Mon,
>>> 03 Apr 2017 09:41:41 -0700
>>> 
>>>
>>> if you are using version 6, then it should have produced a file called
>>> pcc.mgh. This the partial pearson correlation coef.
>>>
>>>
>>>
>>> 2017-04-03 15:40 GMT+01:00 tom parker :
>>>
 Dear Freesurfers,

 I made some correlations between cortical thickness and age in qdec.

 Is it possible to get the correlation coefficient value of this
 analysis?

 I just need to put it in a table with the significant results.

 Thank you so much!

>>>
>>>
>>
>
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Re: [Freesurfer] correlation coefficient R

[Douglas N Greve]

Try something like

mri_segstats --i pcc.mgh --seg cluster.ocn.mgh --excludeid 0 --sum 
cluster.pcc.dat


On 04/07/2017 08:35 PM, tom parker wrote:
> Hi Doug,
>
> Thank you for your answer!
>
> It would be great if you could send me some instructions.
>
> Thanks for the help!
>
> Douglas N Greve 
> 
>  
> Thu, 06 Apr 2017 13:32:07 -0700 
> 
>  
>
>
> I guess you could average it over space (eg, over a cluster). Let me
> know if you want instructions. Otherwise, I'm not sure what to say.
>
>
> 2017-04-04 11:49 GMT+01:00 tom parker  >:
>
> Hi Doug,
>
> Thanks! I realize now I didn't explain myself properly.
>
> I need one single R value for the correlation analysis I made,
> similarly to when I correlate two variables with Pearson's R in a
> statistical package. I have a referee asking me to put it on a
> table with the freesurfer results. Is there a way to get a single
> average R value from the pcc.mgh file?
>
> Thank you so much!
>
> Douglas Greve
> 
> 
> Mon, 03 Apr 2017 18:46:46 -0700
> 
> 
>
>
> Each vertex is a correlation value.
>
>
> 2017-04-04 1:09 GMT+01:00 tom parker  >:
>
> Thanks Doug!
>
> I have version 6 and got a pcc.mgh file.
>
> How can I get a correlation R value from this file?
>
> Thanks again
>
> Douglas N Greve
> 
> 
> Mon, 03 Apr 2017 09:41:41 -0700
> 
> 
>
>
> if you are using version 6, then it should have produced a file called
> pcc.mgh. This the partial pearson correlation coef.
>
>
>
> 2017-04-03 15:40 GMT+01:00 tom parker  >:
>
> Dear Freesurfers,
>
> I made some correlations between cortical thickness and
> age in qdec.
>
> Is it possible to get the correlation coefficient value of
> this analysis?
>
> I just need to put it in a table with the significant results.
>
> Thank you so much!
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] correlation coefficient R

[tom parker]

Hi Doug,

Thank you for your answer!

It would be great if you could send me some instructions.

Thanks for the help!

Douglas N Greve

Thu,
06 Apr 2017 13:32:07 -0700


I guess you could average it over space (eg, over a cluster). Let me
know if you want instructions. Otherwise, I'm not sure what to say.



2017-04-04 11:49 GMT+01:00 tom parker :

> Hi Doug,
>
> Thanks! I realize now I didn't explain myself properly.
>
> I need one single R value for the correlation analysis I made, similarly to 
> when I correlate two variables with Pearson's R in a statistical package.
>
> I have a referee asking me to put it on a table with the freesurfer results. 
> Is there a way to get a single average R value from the pcc.mgh file?
>
> Thank you so much!
>
>
> Douglas Greve
> 
>  Mon,
> 03 Apr 2017 18:46:46 -0700
> 
> Each vertex is a correlation value.
>
>
>
> 2017-04-04 1:09 GMT+01:00 tom parker :
>
>> Thanks Doug!
>>
>> I have version 6 and got a pcc.mgh file.
>>
>> How can I get a correlation R value from this file?
>>
>> Thanks again
>>
>> Douglas N Greve
>> 
>>  Mon,
>> 03 Apr 2017 09:41:41 -0700
>> 
>>
>> if you are using version 6, then it should have produced a file called
>> pcc.mgh. This the partial pearson correlation coef.
>>
>>
>>
>> 2017-04-03 15:40 GMT+01:00 tom parker :
>>
>>> Dear Freesurfers,
>>>
>>> I made some correlations between cortical thickness and age in qdec.
>>>
>>> Is it possible to get the correlation coefficient value of this analysis?
>>>
>>> I just need to put it in a table with the significant results.
>>>
>>> Thank you so much!
>>>
>>
>>
>
___
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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.

Re: [Freesurfer] correlation coefficient R

[Douglas N Greve]

I guess you could average it over space (eg, over a cluster). Let me 
know if you want instructions. Otherwise, I'm not sure what to say.


On 04/04/2017 06:49 AM, tom parker wrote:
> Hi Doug,
> Thanks! I realize now I didn't explain myself properly.
> I need one single R value for the correlation analysis I made, 
> similarly to when I correlate two variables with Pearson's R in a 
> statistical package. I have a referee asking me to put it on a table 
> with the freesurfer results. Is there a way to get a single average R 
> value from the pcc.mgh file?
> Thank you so much!
>
> Douglas Greve 
> 
>  
> Mon, 03 Apr 2017 18:46:46 -0700 
> 
>  
>
>
> Each vertex is a correlation value.
>
> 2017-04-04 1:09 GMT+01:00 tom parker  >:
>
> Thanks Doug!
>
> I have version 6 and got a pcc.mgh file.
>
> How can I get a correlation R value from this file?
>
> Thanks again
>
> Douglas N Greve
> 
> 
> Mon, 03 Apr 2017 09:41:41 -0700
> 
> 
>
>
> if you are using version 6, then it should have produced a file called
> pcc.mgh. This the partial pearson correlation coef.
>
>
>
> 2017-04-03 15:40 GMT+01:00 tom parker  >:
>
> Dear Freesurfers,
>
> I made some correlations between cortical thickness and age in
> qdec.
>
> Is it possible to get the correlation coefficient value of
> this analysis?
>
> I just need to put it in a table with the significant results.
>
> Thank you so much!
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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.

Re: [Freesurfer] correlation coefficient R

[tom parker]

Hi Doug,

Thanks! I realize now I didn't explain myself properly.

I need one single R value for the correlation analysis I made,
similarly to when I correlate two variables with Pearson's R in a
statistical package.

I have a referee asking me to put it on a table with the freesurfer
results. Is there a way to get a single average R value from the
pcc.mgh file?

Thank you so much!


Douglas Greve

Mon,
03 Apr 2017 18:46:46 -0700

Each vertex is a correlation value.



2017-04-04 1:09 GMT+01:00 tom parker :

> Thanks Doug!
>
> I have version 6 and got a pcc.mgh file.
>
> How can I get a correlation R value from this file?
>
> Thanks again
>
> Douglas N Greve
> 
>  Mon,
> 03 Apr 2017 09:41:41 -0700
> 
>
> if you are using version 6, then it should have produced a file called
> pcc.mgh. This the partial pearson correlation coef.
>
>
>
> 2017-04-03 15:40 GMT+01:00 tom parker :
>
>> Dear Freesurfers,
>>
>> I made some correlations between cortical thickness and age in qdec.
>>
>> Is it possible to get the correlation coefficient value of this analysis?
>>
>> I just need to put it in a table with the significant results.
>>
>> Thank you so much!
>>
>
>
___
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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.

Re: [Freesurfer] correlation coefficient R

[tom parker]

Thanks Doug!

I have version 6 and got a pcc.mgh file.

How can I get a correlation R value from this file?

Thanks again

Douglas N Greve

Mon,
03 Apr 2017 09:41:41 -0700


if you are using version 6, then it should have produced a file called
pcc.mgh. This the partial pearson correlation coef.



2017-04-03 15:40 GMT+01:00 tom parker :

> Dear Freesurfers,
>
> I made some correlations between cortical thickness and age in qdec.
>
> Is it possible to get the correlation coefficient value of this analysis?
>
> I just need to put it in a table with the significant results.
>
> Thank you so much!
>
___
Freesurfer mailing list
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.

Re: [Freesurfer] correlation coefficient R

[Douglas N Greve]

if you are using version 6, then it should have produced a file called 
pcc.mgh. This the partial pearson correlation coef.


On 04/03/2017 10:40 AM, tom parker wrote:
> Dear Freesurfers,
>
> I made some correlations between cortical thickness and age in qdec.
>
> Is it possible to get the correlation coefficient value of this analysis?
>
> I just need to put it in a table with the significant results.
>
> Thank you so much!
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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.

[Freesurfer] correlation coefficient R

[tom parker]

Dear Freesurfers,

I made some correlations between cortical thickness and age in qdec.

Is it possible to get the correlation coefficient value of this analysis?

I just need to put it in a table with the significant results.

Thank you so much!
___
Freesurfer mailing list
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.