Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

2016-12-03 Thread Elijah Mak 
Hi Doug,

Thanks. It works! What does each vertex represent in V.mgh?
http://imgur.com/W1RZdKn

Here are the results from the stats. Then, I would like to extract the 1st
component and convert it into label for mri_segstats. How may I do that?

  1   105131.57 105131.5773.79   73.79

  29130.61 114262.18 6.41   80.20

  38052.58 122314.77 5.65   85.85

  45480.79 127795.56 3.85   89.69

  54398.33 132193.89 3.09   92.78

  63504.02 135697.91 2.46   95.24

  72386.62 138084.53 1.68   96.92

  82055.74 140140.27 1.44   98.36

  91603.79 141744.06 1.13   99.48

 10 734.89 142478.95 0.52  100.00

 11   0.00 142478.95 0.00  100.00


Thanks.

Best Wishes,
Elijah




Re: [Freesurfer] PCA on PET / Thickness in Freesurfer
<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50417.html>
2016-12-02
<http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu=date:20161202=newest=1>
 Thread
<http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu=subject:%22%5C%5BFreesurfer%5C%5D+PCA+on+PET+%5C%2F+Thickness+in+Freesurfer%22=newest=1>
 Douglas N Greve
<http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu=from:%22Douglas+N+Greve%22=newest=1>

You can run it like that or with --osgm (instead of --fsgd and --C),
osgm = one sample group mean.


On 12/01/2016 07:13 PM, Foo Keat Mak wrote:
> Hi Doug,
> I have pasted the correspondences below. My question is, if I want to
> identify the PCs in a group for a single modality (PET), how should I
> run the mri_glmfit? A single group design with A contrast of 1 0 (for
> a nuisance covariate)?
> Thanks !
> Elijah
> Doug:
> For within modality, you can add --pca to mri_glmfit (run it with
> --help to get more info). We do not have ICA tools in FS.
> On 12/01/2016 02:04 PM, Foo Keat Mak wrote: > Hi Freesurfer Team, > >
> For a given group, I want to look at the covariance patterns between >
> thickness and PET. Within Freesurfer, what are some general workflow >
> tips on how I could go about performing PCA (within modality) or joint
> > ICA analyses looking at the covariance patterns across modalities?
> Is > the -pca flag a good starting point? > > Any feedback is
> appreciated! > > Thanks a lot. > > Best Wishes, > Elijah > > >
> ___ > 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/
> ___ Freesurfer mailing
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>
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>
>
> Sent from my iPad
>
> On 1 Dec 2016, at 23:30, Foo Keat Mak  > wrote:
>
>> Thanks Doug. Does that mean that a one group design? With a contrast
>> of 1 0 (adjusting for one variable)?
>>
>>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR centergr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] PCA on PET / Thickness in Freesurfer
<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50407.html>
2016-12-01
<http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu=date:20161201=newest=1>
 Thread
<http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu=subject:%22%5C%5BFreesurfer%5C%5D+PCA+on+PET+%5C%2F+Thickness+in+Freesurfer%22=newest=1>
 Foo Keat Mak
<http://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu=from:%22Foo+Keat+Mak%22=newest=1>

Hi

Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

2016-12-02 Thread Douglas N Greve 
You can run it like that or with --osgm (instead of --fsgd and --C), 
osgm = one sample group mean.


On 12/01/2016 07:13 PM, Foo Keat Mak wrote:
> Hi Doug,
> I have pasted the correspondences below. My question is, if I want to 
> identify the PCs in a group for a single modality (PET), how should I 
> run the mri_glmfit? A single group design with A contrast of 1 0 (for 
> a nuisance covariate)?
> Thanks !
> Elijah
> Doug:
> For within modality, you can add --pca to mri_glmfit (run it with 
> --help to get more info). We do not have ICA tools in FS.
> On 12/01/2016 02:04 PM, Foo Keat Mak wrote: > Hi Freesurfer Team, > > 
> For a given group, I want to look at the covariance patterns between > 
> thickness and PET. Within Freesurfer, what are some general workflow > 
> tips on how I could go about performing PCA (within modality) or joint 
> > ICA analyses looking at the covariance patterns across modalities? 
> Is > the -pca flag a good starting point? > > Any feedback is 
> appreciated! > > Thanks a lot. > > Best Wishes, > Elijah > > > 
> ___ > 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/ 
> ___ 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.
>
>
> Sent from my iPad
>
> On 1 Dec 2016, at 23:30, Foo Keat Mak  > wrote:
>
>> Thanks Doug. Does that mean that a one group design? With a contrast 
>> of 1 0 (adjusting for one variable)?
>>
>>
>
>
> ___
> 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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Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

2016-12-01 Thread Foo Keat Mak 
Hi Doug,


I have pasted the correspondences below. My question is, if I want to identify 
the PCs in a group for a single modality (PET), how should I run the 
mri_glmfit? A single group design with A contrast of 1 0 (for a nuisance 
covariate)?


Thanks !


Elijah



Doug:

For within modality, you can add --pca to mri_glmfit (run it with --help
to get more info). We do not have ICA tools in FS.




On 12/01/2016 02:04 PM, Foo Keat Mak wrote:
> Hi Freesurfer Team,
>
> For a given group, I want to look at the covariance patterns between
> thickness and PET.  Within Freesurfer, what are some general workflow
> tips on how I could go about performing PCA (within modality) or joint
> ICA analyses looking at the covariance patterns across modalities?  Is
> the -pca flag a good starting point?
>
> Any feedback is appreciated!
>
> Thanks a lot.
>
> Best Wishes,
> Elijah
>
>
> ___
> 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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Sent from my iPad

On 1 Dec 2016, at 23:30, Foo Keat Mak 
> wrote:

Thanks Doug. Does that mean that a one group design? With a contrast of 1 0 
(adjusting for one variable)?


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Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

2016-12-01 Thread Douglas N Greve 
sorry, can you repost with previous correspondence?


On 12/01/2016 06:30 PM, Foo Keat Mak wrote:
> Thanks Doug. Does that mean that a one group design? With a contrast 
> of 1 0 (adjusting for one variable)?
>
>
>
>
> ___
> 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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Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

2016-12-01 Thread Foo Keat Mak 
Thanks Doug. Does that mean that a one group design? With a contrast of 1 0 
(adjusting for one variable)?


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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] PCA on PET / Thickness in Freesurfer

2016-12-01 Thread Douglas N Greve 
For within modality, you can add --pca to mri_glmfit (run it with --help 
to get more info). We do not have ICA tools in FS.


On 12/01/2016 02:04 PM, Foo Keat Mak wrote:
> Hi Freesurfer Team,
>
> For a given group, I want to look at the covariance patterns between 
> thickness and PET.  Within Freesurfer, what are some general workflow 
> tips on how I could go about performing PCA (within modality) or joint 
> ICA analyses looking at the covariance patterns across modalities?  Is 
> the -pca flag a good starting point?
>
> Any feedback is appreciated!
>
> Thanks a lot.
>
> Best Wishes,
> Elijah
>
>
> ___
> 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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