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Hello Guodong,

consider as an analogy a two-sample t-test, where we simply compare two groups A and B:

If formulated as a regression problem, a commonly used model matrix for this test (but others are possible, too) will consist of two columns, one being all ones (the intercept), the other being zero for group A and one for group B.

The beta value for the first regressor should reflect the mean for group A (which is chosen as the reference group), and the beta value for the second regressor should reflect the difference between group A and B, which is the primary interest for this comparison. To get the mean for group B, one would need to add the beta weights of the two regressors.

The LME design matrices follow the same logic.

Alternatively, as said before, other design matrices are possible. In the above toy example, one could also use a matrix with two columns, where column 1 is one for group A and zero for group B, and column 2 is zero for group A and one for group B, thus omitting the overall intercept. Then, the beta weights would directly reflect the means of A and B. To get the difference between groups A and B, one would need to subtract the beta weights.

Mathematically, the two above models are equivalent. This also implies that one should not specify a model where there is an intercept, a regressor for group A, and a regressor for group B, because in this case, the regressors would be linearly dependent. Since having an overall intercept is advantageous (especially in more complex modelling situations than this toy example), the first model is the preferred one.

Hope this helps,

Kersten

On So, 2019-11-03 at 16:33 +0800, Liu Guodong wrote:

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Dear Kersten:  The β1 and β2 in the tutorial model is the regressing coefficients for all the subjects not only for the control subjects because all the intercept are one. I wonder why the reference group is control group in this case?

Thanks in advance.

Best regards, Guodong

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在 2019年10月25日，上午12:00，freesurfer-request@nmr.mgh.harvard.edu 写道：

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Today's Topics:

1. time point exlusion file exceed nframes (Lauri Tuominen)   2. Re: time point exlusion file exceed nframes      (Greve, Douglas N.,Ph.D.)   3. Re: Learning fsfast tutorial (Greve, Douglas N.,Ph.D.)   4. Re: LME model contrast matrix (Diers, Kersten /DZNE)   5. Re: Learning fsfast tutorial (Renew Andrade)   6. Re: Learning dti processing tutorial (Renew Andrade)   7. mri_cvs_register error while diffusion imaging processi ng      (Renew Andrade)

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Message: 1 Date: Wed, 23 Oct 2019 17:34:59 +0000 From: Lauri Tuominen ljtuom@utu.fi Subject: [Freesurfer] time point exlusion file exceed nframes To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.ed u> Message-ID: 6506F69C-782A-4074-A898-17E58814EF58@utu.fi Content-Type: text/plain; charset="utf-8"

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Dear Freesurfers, I am running resting state analysis. I have TR 2.3, and 209 time points/frames, total length of the scan 483 seconds. I don?t drop any frames from the beginning ( nskip = 0 ).

For one subject, the last two time points are motion outliers. So my tpef file includes numbers 478.4 and 480.7. When I run selxavg3- sess, I get the error time point exlusion file exceed nframes.

I can?t figure out where the bug might be. So once again I would really appreciate your help!  Thanks  Lauri Tuominen

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Message: 2 Date: Thu, 24 Oct 2019 03:28:21 +0000 From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] time point exlusion file exceed nframes To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.ed u> Message-ID: fee25413-e204-29d7-27c0-a69427052343@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"

Hi Lauri, I think this comes down to whether you start counting from 0  or 1. FSFAST starts from 0, so the time of? time point N is N*TR. The  maximum you can have is N=208, and so the max time would be 478.4. Your  480.7 exceeds this limit. doug

On 10/23/2019 1:34 PM, Lauri Tuominen wrote:

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Dear Freesurfers, I am running resting state analysis. I have TR 2.3, and 209 time points/frames, total length of the scan 483 seconds. I don?t drop any frames from the beginning ( nskip = 0 ).

For one subject, the last two time points are motion outliers. So my tpef file includes numbers 478.4 and 480.7. When I run selxavg3-sess, I get the error time point exlusion file exceed nframes.

I can?t figure out where the bug might be. So once again I would really appreciate your help! Thanks Lauri Tuominen

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Message: 3 Date: Thu, 24 Oct 2019 03:29:14 +0000 From: "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Subject: Re: [Freesurfer] Learning fsfast tutorial To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.ed u> Message-ID: a582080c-85f2-9a05-6dad-d4cfba600faf@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"

look in sess01/bold, you should see 001 and 002. Do you?

On 10/22/2019 9:40 AM, Renew Andrade wrote:

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Dear experts: I am trying to run preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run But the outcome is ERROR: no run directories found.

What could be wrong? If you need more information let me know!

Sincerely, Andrade.

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