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Qasim Bukhari <[log in to unmask]> escreveu no dia quarta, 29/08/2018 à(s) 17:41:

Dear Anderson

a couple of quick questions on it

Is this procedure also valid for resting state data of two different conditions?
How can this subtraction technique be used as design matrix inside the FSL Nets ? For running FSL Nets, what would be our difference images, since the inputs are the melodic or dr_stage1 files.
Thanks for your help

best

Qasim

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Anderson M. Winkler <[log in to unmask]>
Sent: Thursday, August 2, 2018 9:53 PM
To: [log in to unmask]
Subject: Re: [FSL] Doubts in our Design Matrix

Hi Daniela,

Although it's possible to put all data in a large design, perhaps you will prefer a more parsimonious strategy that is:

1) Compute the differences t2-t1, fu-t2 and fu-t1, thus having three 4D NIFTI files (each one having one 3D per subject, all in the same order).

2) Assemble a one-way ANOVA as in the manual, specifying your 4 groups as you have them: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#ANOVA:_1-factor_4-levels__.281-way_between-subjects_ANOVA.29

The contrasts would however, be different. Probably you'll want something as

C1: [1 1 -1 1]

C2: [1 -1 1 -1]

C3: [1 -1 -1 1]

(and the negative versions of these).

Hope this helps...

All the best,

Anderson

On Tue, 31 Jul 2018 at 20:33, Daniela Valério <[log in to unmask]> wrote:

Hi FSL experts and Anderson,

Sorry for the spam, but I really appreciate your help in this topic. I'm a little lost in what is the best method to use.

Thanks in advance for any help,

Daniela Valério

2018-07-26 14:33 GMT+01:00 Daniela Valério <[log in to unmask]>:

Dear Anderson,

Sorry for my poor information. I have more participants, but let's think of 5 participants for each group to be easier. We have 4 groups of participants: cond1, cond2, control1, control2, each group has different participants. However, each participant was measured 3 times: time1, time2 and Follow up. Thus, we have different subjects in each group but the same subjects within sessions. We would like to compare time1-time2, time1-Fu and time2-Fu conditions through an ANOVA 2X4. Is this clear? Please tell me if it's not clear enough, then I can try to explain in a different way.

As mentioned above, we believe that one of these two designs can be the one that we need. Here, we want to compare time1-time2 for the 4 groups (each one with 5 participants).

Can you check, please?

Design1:

1 1 0 1 0
1 1 0 1 0
1 1 0 1 0
1 1 0 1 0
1 1 0 1 0
1 0 1 0 1
1 0 1 0 1
1 0 1 0 1
1 0 1 0 1
1 0 1 0 1
1 -1 -1 -1 -1
1 -1 -1 -1 -1
1 -1 -1 -1 -1
1 -1 -1 -1 -1
1 -1 -1 -1 -1
1 0 0 0 0
1 0 0 0 0
1 0 0 0 0
1 0 0 0 0
1 0 0 0 0
-1 1 0 -1 0
-1 1 0 -1 0
-1 1 0 -1 0
-1 1 0 -1 0
-1 1 0 -1 0
-1 0 1 0 -1
-1 0 1 0 -1
-1 0 1 0 -1
-1 0 1 0 -1
-1 0 1 0 -1
-1 -1 -1 1 1
-1 -1 -1 1 1
-1 -1 -1 1 1
-1 -1 -1 1 1
-1 -1 -1 1 1
-1 0 0 0 0
-1 0 0 0 0
-1 0 0 0 0
-1 0 0 0 0
-1 0 0 0 0

Design 2:

1 0 0 0 1 0 0 0 0 0 0 0
1 0 0 0 0 1 0 0 0 0 0 0
1 0 0 0 0 0 1 0 0 0 0 0
1 0 0 0 0 0 0 1 0 0 0 0
0 1 0 0 1 0 0 0 0 0 0 0
0 1 0 0 0 1 0 0 0 0 0 0
0 1 0 0 0 0 1 0 0 0 0 0
0 1 0 0 0 0 0 1 0 0 0 0
0 0 1 0 1 0 0 0 0 0 0 0
0 0 1 0 0 1 0 0 0 0 0 0
0 0 1 0 0 0 1 0 0 0 0 0
0 0 1 0 0 0 0 1 0 0 0 0
0 0 0 1 1 0 0 0 0 0 0 0
0 0 0 1 0 1 0 0 0 0 0 0
0 0 0 1 0 0 1 0 0 0 0 0
0 0 0 1 0 0 0 1 0 0 0 0
-1 0 0 0 0 0 0 0 1 0 0 0
-1 0 0 0 0 0 0 0 0 1 0 0
-1 0 0 0 0 0 0 0 0 0 1 0
-1 0 0 0 0 0 0 0 0 0 0 1
0 -1 0 0 0 0 0 0 1 0 0 0
0 -1 0 0 0 0 0 0 0 1 0 0
0 -1 0 0 0 0 0 0 0 0 1 0
0 -1 0 0 0 0 0 0 0 0 0 1
0 0 -1 0 0 0 0 0 1 0 0 0
0 0 -1 0 0 0 0 0 0 1 0 0
0 0 -1 0 0 0 0 0 0 0 1 0
0 0 -1 0 0 0 0 0 0 0 0 1
0 0 0 -1 0 0 0 0 1 0 0 0
0 0 0 -1 0 0 0 0 0 1 0 0
0 0 0 -1 0 0 0 0 0 0 1 0
0 0 0 -1 0 0 0 0 0 0 0 1

Thanks in advance for your help,

Daniela Valério

2018-07-26 2:08 GMT+01:00 Anderson M. Winkler <[log in to unmask]>:

Hi Daniela,

Sorry, could you give more details? How many measurements each participant has (2 for the two timepoints, or 8 for the two timepoints and 4 conditions)? Is it that you have 5 participants overall ("scanners") or each participant was scanned 5 times at each timepoint and condition? Or are "cond" and "control" experimental groups of subjects?

Also, are there nuisance variables you'd like to accommodate in the model?

All the best,

Anderson

On Mon, 23 Jul 2018 at 12:14, Daniela Valério <[log in to unmask]> wrote:

Dear Experts,

Sorry for the spam, but I'm having difficulties to figure out if this matrix makes sense in my experiment. Can you help me, please?

Thanks in advance for any help,

Best,

Daniela Valério

2018-07-19 12:42 GMT+01:00 Daniela Valério <[log in to unmask]>:

I realized that may is difficult to open the design matrices. So, here are the two designs that we need help to analyze:

Design1:

1 1 0 1 0
1 1 0 1 0
1 1 0 1 0
1 1 0 1 0
1 1 0 1 0
1 0 1 0 1
1 0 1 0 1
1 0 1 0 1
1 0 1 0 1
1 0 1 0 1
1 -1 -1 -1 -1
1 -1 -1 -1 -1
1 -1 -1 -1 -1
1 -1 -1 -1 -1
1 -1 -1 -1 -1
1 0 0 0 0
1 0 0 0 0
1 0 0 0 0
1 0 0 0 0
1 0 0 0 0
-1 1 0 -1 0
-1 1 0 -1 0
-1 1 0 -1 0
-1 1 0 -1 0
-1 1 0 -1 0
-1 0 1 0 -1
-1 0 1 0 -1
-1 0 1 0 -1
-1 0 1 0 -1
-1 0 1 0 -1
-1 -1 -1 1 1
-1 -1 -1 1 1
-1 -1 -1 1 1
-1 -1 -1 1 1
-1 -1 -1 1 1
-1 0 0 0 0
-1 0 0 0 0
-1 0 0 0 0
-1 0 0 0 0
-1 0 0 0 0

Design 2:

1 0 0 0 1 0 0 0 0 0 0 0
1 0 0 0 0 1 0 0 0 0 0 0
1 0 0 0 0 0 1 0 0 0 0 0
1 0 0 0 0 0 0 1 0 0 0 0
0 1 0 0 1 0 0 0 0 0 0 0
0 1 0 0 0 1 0 0 0 0 0 0
0 1 0 0 0 0 1 0 0 0 0 0
0 1 0 0 0 0 0 1 0 0 0 0
0 0 1 0 1 0 0 0 0 0 0 0
0 0 1 0 0 1 0 0 0 0 0 0
0 0 1 0 0 0 1 0 0 0 0 0
0 0 1 0 0 0 0 1 0 0 0 0
0 0 0 1 1 0 0 0 0 0 0 0
0 0 0 1 0 1 0 0 0 0 0 0
0 0 0 1 0 0 1 0 0 0 0 0
0 0 0 1 0 0 0 1 0 0 0 0
-1 0 0 0 0 0 0 0 1 0 0 0
-1 0 0 0 0 0 0 0 0 1 0 0
-1 0 0 0 0 0 0 0 0 0 1 0
-1 0 0 0 0 0 0 0 0 0 0 1
0 -1 0 0 0 0 0 0 1 0 0 0
0 -1 0 0 0 0 0 0 0 1 0 0
0 -1 0 0 0 0 0 0 0 0 1 0
0 -1 0 0 0 0 0 0 0 0 0 1
0 0 -1 0 0 0 0 0 1 0 0 0
0 0 -1 0 0 0 0 0 0 1 0 0
0 0 -1 0 0 0 0 0 0 0 1 0
0 0 -1 0 0 0 0 0 0 0 0 1
0 0 0 -1 0 0 0 0 1 0 0 0
0 0 0 -1 0 0 0 0 0 1 0 0
0 0 0 -1 0 0 0 0 0 0 1 0
0 0 0 -1 0 0 0 0 0 0 0 1

We really appreciate your help,

Best Regards,

Daniela Valério

2018-07-19 12:07 GMT+01:00 Daniela Valério <[log in to unmask]>:

Dear FSL experts,

We are having difficulties to find the correct design matrix for our data. In the following schema, we have a brief explanation of our experiment:

We want to do an ANOVA 2 (the time 1 and 2) x 4 (cond1, cond2, control1, control2). We have in the attachment two design matrices that can fit in our data. Can you FSL experts check and tell us which one is the best?

Thanks for your help and support,

Sincerely,

Daniela Valério

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