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This is a discussion forum for issues related to the SwE Toolbox for SPM, an analysis tool for longitudinal and repeated measures brain imaging data. SwE uses a marginal model approach (no subject-specific indicator regressors), ordinary least square estimators of population regression parameters and the sandwich estimator for standard errors. For more information visit http://nisox.org/Software/SwE.

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yann...@gmail.com, Thomas Nichols3

Mar 14

Setting up longitudinal TBSS analysis using SwE for FSL

Thanks Tom. As responded to the FSLlist, it ran just fine. Sorry for the cross-posting, I thought the

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Setting up longitudinal TBSS analysis using SwE for FSL

Thanks Tom. As responded to the FSLlist, it ran just fine. Sorry for the cross-posting, I thought the

Mar 14

Nathan Petro, Thomas Nichols3

Feb 3

Question about modeling in longitudinal analysis

Tom, Thank you so much for the response, and our apologies for the rather delayed response. This is

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Question about modeling in longitudinal analysis

Tom, Thank you so much for the response, and our apologies for the rather delayed response. This is

Feb 3

11/1/24

Only 1 contrast allowed with wild boostrapping?

Hello, We are running a 4x2x2 model: 1st factor - 3 levels, within subjects - time1,time2,time3 2nd

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Only 1 contrast allowed with wild boostrapping?

Hello, We are running a 4x2x2 model: 1st factor - 3 levels, within subjects - time1,time2,time3 2nd

11/1/24

Evelyn M, … Aimee Flores7

10/11/24

within-subject intervention design - covariates of no interest

Dear Evelyn and Tom, I have a very similar design. I did therefore the following matrix. BCI is the

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within-subject intervention design - covariates of no interest

Dear Evelyn and Tom, I have a very similar design. I did therefore the following matrix. BCI is the

10/11/24

10/9/24

2 groups and 2 within-subject factors

In particular, I was confused by other comments in this forum in which they added the intercept, as

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2 groups and 2 within-subject factors

In particular, I was confused by other comments in this forum in which they added the intercept, as

10/9/24

3/19/24

3 by 3 within-subjects setup

Dear SwE users, I am trying to set up a basic (no covariate) model for a full within-subjects design,

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3 by 3 within-subjects setup

Dear SwE users, I am trying to set up a basic (no covariate) model for a full within-subjects design,

3/19/24

Chloe Cheung, Thomas Nichols8

3/3/24

FWE Corrected Results vs Uncorrected Results Display Discrepancy

Super! On Sun, 3 Mar 2024 at 05:28, Chloe Cheung <chloec...@gmail.com> wrote: Dear Tom, I

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FWE Corrected Results vs Uncorrected Results Display Discrepancy

Super! On Sun, 3 Mar 2024 at 05:28, Chloe Cheung <chloec...@gmail.com> wrote: Dear Tom, I

3/3/24

3/1/24

Issues with defining contrast in mixed model

Dear SwE experts, I hope this email finds you well. This is the first time I am using the SwE

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Issues with defining contrast in mixed model

Dear SwE experts, I hope this email finds you well. This is the first time I am using the SwE

3/1/24

John C. Flournoy

1/19/24

Script or batch to automate creating contrast stats

Hi there, I was wondering if anyone knows a way (eg, which swe_ function to call) to produce contrast

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Script or batch to automate creating contrast stats

Hi there, I was wondering if anyone knows a way (eg, which swe_ function to call) to produce contrast

1/19/24

Guillermina Griffa

7/6/23

Clusterwise, TFCE Vs. voxelwise inference

Hi Tom, I conducted a longitudinal experiment (n=28) in which we acquired Diffusion Magnetic

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Clusterwise, TFCE Vs. voxelwise inference

Hi Tom, I conducted a longitudinal experiment (n=28) in which we acquired Diffusion Magnetic

7/6/23

elisa cargnelutti

5/31/23

Dear SwE experts, I apologize for this question. I ran WB, voxel-wise interference, to explore

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Dear SwE experts, I apologize for this question. I ran WB, voxel-wise interference, to explore

5/31/23

Benjamin Kay, Thomas Nichols4

5/19/23

TFCE and bootstrap

Dear Benjamin, On 18 May 2023, at 19:39, Benjamin Kay <benj...@benkay.net> wrote: Thank you

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TFCE and bootstrap

Dear Benjamin, On 18 May 2023, at 19:39, Benjamin Kay <benj...@benkay.net> wrote: Thank you

5/19/23

4/5/23

Differences in Functional Connectivity using SwE

Hello, I am trying to come up with the correct set up for the design.mat, design.con and design.fts

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Differences in Functional Connectivity using SwE

Hello, I am trying to come up with the correct set up for the design.mat, design.con and design.fts

4/5/23

2/14/23

Adding scan list in .mat format to the batch

Hello! Is there another platform where I can ask for technical help on this toolbox? Thanks! On

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Adding scan list in .mat format to the batch

Hello! Is there another platform where I can ask for technical help on this toolbox? Thanks! On

2/14/23

1/23/23

Longitudinal Analysis Model

We are investigating the effect of age across 3 visits on MEG brain activity. We are wanting to know

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Longitudinal Analysis Model

We are investigating the effect of age across 3 visits on MEG brain activity. We are wanting to know

1/23/23

Susanne Stickel, Grant Tays2

1/20/23

Longitudinal VBM with covariates

Hi Susanne, I'm not particularly an expert on all of this yet, but I've been working with SwE

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Longitudinal VBM with covariates

Hi Susanne, I'm not particularly an expert on all of this yet, but I've been working with SwE

1/20/23

Elisa Cargnelutti, Manfred Klöbl2

12/22/22

covariate mean-centering

Dear Elisa, you mean-center the tumor volume only within the group of patients. The covariate stays 0

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covariate mean-centering

Dear Elisa, you mean-center the tumor volume only within the group of patients. The covariate stays 0

12/22/22

11/14/22

SwE Repeated Measures Question

Hello, I had a, I think, brief question regarding SwE. I've been using it extensively now

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SwE Repeated Measures Question

Hello, I had a, I think, brief question regarding SwE. I've been using it extensively now

11/14/22

8/11/22

save thresholded result maps

Hi, How do you save a thresholded nii image of SwE results to use in another MRI viewer? I have tried

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save thresholded result maps

Hi, How do you save a thresholded nii image of SwE results to use in another MRI viewer? I have tried

8/11/22

8/1/22

Multiple sessions onsets.mat file and realignment parameters .txt file

Dear Prs. I am a PhD student in Paris, working on functional MRI data. I am now analyzing old data

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Multiple sessions onsets.mat file and realignment parameters .txt file

Dear Prs. I am a PhD student in Paris, working on functional MRI data. I am now analyzing old data

8/1/22

5/4/22

Error in swe_DesRep

Hi! I'm relatively new to SwE, but I would like to use it for my current project which is a

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Error in swe_DesRep

Hi! I'm relatively new to SwE, but I would like to use it for my current project which is a

5/4/22

4/13/22

Longitudinal Analysis Model

We are investigating the effect of age across 3 visits on MEG brain activity. We are wanting to know

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Longitudinal Analysis Model

We are investigating the effect of age across 3 visits on MEG brain activity. We are wanting to know

4/13/22

Agnieszka Kulesza

3/4/22

no equal distances in time between visits

Hi all, I am trying to run a longitudinal analysis. In a nutshell, I have two groups (experimental:

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no equal distances in time between visits

Hi all, I am trying to run a longitudinal analysis. In a nutshell, I have two groups (experimental:

3/4/22

Eleni Panagoulas

2/20/22

Run model error

Dear Dr Nichols, I am carrying out a longitudinal analysis with stroke patients that were followed up

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Run model error

Dear Dr Nichols, I am carrying out a longitudinal analysis with stroke patients that were followed up

2/20/22

Haris Styliadis, … Grant Tays5

2/2/22

Bootstrapping/batch results

Just following up with this to see if there has been an update. Not associated with the original post

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Bootstrapping/batch results

Just following up with this to see if there has been an update. Not associated with the original post

2/2/22

Alon Itzkovitch

1/13/22

functional connectivity differences using SwE

I have a resting state data of two groups with five timepoints. I tried to measure the differences

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functional connectivity differences using SwE

I have a resting state data of two groups with five timepoints. I tried to measure the differences

1/13/22

philip Joadavi3

12/19/21

HELP for error Dependency source available, but is missing required output.

Just in case someone else got to this issue, I solved it by reinstalling the spm12. On Saturday,

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HELP for error Dependency source available, but is missing required output.

Just in case someone else got to this issue, I solved it by reinstalling the spm12. On Saturday,

12/19/21

Anouk van der Straten

12/6/21

small sample correction and missing data

Dear SwE experts, I have done an fMRI experiment looking at the neuroimaging effects of different

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small sample correction and missing data

Dear SwE experts, I have done an fMRI experiment looking at the neuroimaging effects of different

12/6/21

Beatriz Puerta Catoira

11/22/21

Multiple covariates example file

Dear Bryan and Thomas, I´m trying to create a design matrix for a study with 2 sessions and 2 types

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Multiple covariates example file

Dear Bryan and Thomas, I´m trying to create a design matrix for a study with 2 sessions and 2 types

11/22/21

Grant Tays, Thomas Nichols3

11/8/21

Brain Behavior Correlations in SwE

Dr. Nichols, Thank you for responding!! This has been very helpful! Just to follow up on that, would

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Brain Behavior Correlations in SwE

Dr. Nichols, Thank you for responding!! This has been very helpful! Just to follow up on that, would

11/8/21

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