There are no rules for choosing the number. Usually the first couple have most of the variance but it looks like yours are spread out a bit. It looks like you reach a point of diminishing returns after 4 or so.

On 01/14/2016 03:43 PM, Afzal, Afsana wrote:

Hi Doug,

These are the first few lines of the wm.dat.pca-stats.dat file:

1 143481216.00 143481216.00 4.06 4.06 2 77359288.00 220840504.00 2.19 6.25 3 42542944.00 263383448.00 1.20 7.46 4 26329902.00 289713350.00 0.75 8.20 5 21830372.00 311543722.00 0.62 8.82 6 19145688.00 330689410.00 0.54 9.36 7 18512178.00 349201588.00 0.52 9.89

According to the functional connectivity tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...), usually only the first 5 components are used for white matter regression. However, if I understand correctly, it looks like the first five components only remove ~8.82% cumulative variance, is that correct? If so, how should I go about choosing components for white matter regression?

Thanks,

Afsana

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Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, January 13, 2016 12:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Interpreting white matter regressor dat file

here you go (1) component number (2) variance spanned by that component (3) cumulative variance spanned up to that component (4) percent variance spanned by that component (5) cumulative percent variance spanned up to that component

On 01/13/2016 09:56 AM, Afzal, Afsana wrote:

...

Hi,

I have generated white matter regressor files for resting state analysis using fcseed-config and fcseed-sess. The resulting files include: wm.dat, wm.dat.pca-stats.dat and wm.dat.log.

How do I interpret the wm.dat.pca-stats.dat file? There are 388 numbered rows (I'm guessing one per acquisition since # of acquisitions is 388?) and five columns. What do the columns represent?

Thanks for your help!

• Afsana

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*Afsana Afzal* Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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