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Aaron's fMRI matlab tools.

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This group is primarily for those using GLM_Flex, FIVE (formerly OrthoView) or SPM8_AutoProcess. I'm hoping that this group will help plug some of the holes caused by my woeful lack of documentation. Please feel free to ask questions, report bugs, request features, and recommend new tools.

-Aaron

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5/6/23

preprocessing before TBR

Dear Aaron When conducting TBR, do we need to do nuisance covariate removal and wavelet despiking (

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preprocessing before TBR

Dear Aaron When conducting TBR, do we need to do nuisance covariate removal and wavelet despiking (

5/6/23

Lorie-Marlène Brault Foisy, Aaron Schultz7

8/19/20

Can't find the utility package to download FIVE

Hey Aaron, I have been able to open my results with FIVE. However, I am not able to get the peak info

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Can't find the utility package to download FIVE

Hey Aaron, I have been able to open my results with FIVE. However, I am not able to get the peak info

8/19/20

Samantha Maltezos, Aaron Schultz4

3/8/20

I've figured out the problem. This is wrong: dat.Group = cell(402,1). It is supposed to be dat.

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I've figured out the problem. This is wrong: dat.Group = cell(402,1). It is supposed to be dat.

3/8/20

Geneviève Allaire-Duquette, … Pauline FAVRE4

11/22/19

FIVE startup error

Hi there, I have the same problem but I can't find where to download the "Utility package

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FIVE startup error

Hi there, I have the same problem but I can't find where to download the "Utility package

11/22/19

11/8/19

column headers in voxelstats

Hi all, perhaps someone can please tell me what the column headers are for the voxelstats output. I

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column headers in voxelstats

Hi all, perhaps someone can please tell me what the column headers are for the voxelstats output. I

11/8/19

Harry Moore, Aaron Schultz3

11/4/19

corrections in FIVE vs peak info

Hi again Aaron, I have been looking at the 'voxelstats' variable created by peak_nii and

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corrections in FIVE vs peak info

Hi again Aaron, I have been looking at the 'voxelstats' variable created by peak_nii and

11/4/19

aaron, Aaron Schultz2

10/22/19

where to download software?

Looks like the wiki page crashed back in august, so I will need to go restore it. You can download

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where to download software?

Looks like the wiki page crashed back in august, so I will need to go restore it. You can download

10/22/19

Harry Moore, Aaron Schultz3

10/4/19

degrees of freedom

Hi Aaron, I think that does help, thanks for taking the time to explain. So therefore I assume that

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degrees of freedom

Hi Aaron, I think that does help, thanks for taking the time to explain. So therefore I assume that

10/4/19

Caroline Landelle

10/1/19

One way Anova (4 levels) and Conjunction

Dear users, I made a one-way Anova including repeated mesures: I.Model = 'con_Mod + random(SS|

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One way Anova (4 levels) and Conjunction

Dear users, I made a one-way Anova including repeated mesures: I.Model = 'con_Mod + random(SS|

10/1/19

Monica Leslie, MCLAREN, Donald6

9/28/19

FWE-corrected p values in peak_nii

Hi Monica, [voxels voxelstats clusterstats sigthresh regions map parameters UID] should be [voxels

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FWE-corrected p values in peak_nii

Hi Monica, [voxels voxelstats clusterstats sigthresh regions map parameters UID] should be [voxels

9/28/19

Mathieu Lesourd, Aaron Schultz5

7/16/19

Error with GLM_Flex_FAST4

I'm not quite sure what is going on, and it is difficult to determine remotely. Based on the

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Error with GLM_Flex_FAST4

I'm not quite sure what is going on, and it is difficult to determine remotely. Based on the

7/16/19

Haris Styliadis, Aaron Schultz4

6/3/19

GLMFlex to GLMFlexFast

Hi Aaron, I have corrected the size of the variables for 116 input files. Now I get the following

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GLMFlex to GLMFlexFast

Hi Aaron, I have corrected the size of the variables for 116 input files. Now I get the following

6/3/19

Payal Arya, Aaron Schultz16

6/3/19

scripting help for 2 within subject factor design

Ok, It looks like this is a label mask. You should turn it into a binary mask, and then you can set I

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scripting help for 2 within subject factor design

Ok, It looks like this is a label mask. You should turn it into a binary mask, and then you can set I

6/3/19

Haris Styliadis, Aaron Schultz2

5/29/19

To start this code is for the older version of GLM_Flex, not the newer GLM_Flex_Fast. Please see here

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To start this code is for the older version of GLM_Flex, not the newer GLM_Flex_Fast. Please see here

5/29/19

Payal Arya, Aaron Schultz2

5/23/19

2x2 within subject design for Zebra finch

The GLM_Flex tools are better suited to this analysis, particularly if you want to evaluate main

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2x2 within subject design for Zebra finch

The GLM_Flex tools are better suited to this analysis, particularly if you want to evaluate main

5/23/19

soni...@gmail.com, Aaron Schultz3

3/19/19

Covariate in GLMFLEX

It's still not entirely clear what you are after with your model. Education is presumably not a

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Covariate in GLMFLEX

It's still not entirely clear what you are after with your model. Education is presumably not a

3/19/19

Kevin Tan, Aaron Schultz2

3/14/19

Missing files/folders in MRtools_2018-03-17 package?

I think it's just the DataFiles that are missing, and it should be fine to use the prior version

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Missing files/folders in MRtools_2018-03-17 package?

I think it's just the DataFiles that are missing, and it should be fine to use the prior version

3/14/19

Adam Teed, Aaron Schultz2

12/6/18

Checking factor level order

Please see this post: https://groups.google.com/forum/#!searchin/fmri_matlab_tools/Contrast$20

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Checking factor level order

Please see this post: https://groups.google.com/forum/#!searchin/fmri_matlab_tools/Contrast$20

12/6/18

Alexandre Obert, Aaron Schultz3

10/25/18

Thanks! Alexandre Le jeudi 25 octobre 2018 18:08:58 UTC+2, Aaron Schultz a écrit : You can download

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Thanks! Alexandre Le jeudi 25 octobre 2018 18:08:58 UTC+2, Aaron Schultz a écrit : You can download

10/25/18

10/12/18

GLM F F results from subset of contrasts images too optimistic?

Hello Aaron, I have a 2x5 mixed design (Drug_con*stimulus + random(subID|stimulus)) for which I am

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GLM F F results from subset of contrasts images too optimistic?

Hello Aaron, I have a 2x5 mixed design (Drug_con*stimulus + random(subID|stimulus)) for which I am

10/12/18

Jan Beucke, Aaron Schultz8

10/2/18

reporting exact, FDR corrected p-values for results obtained with GLMFlex/FIVE

I would follow up with Donald McLaren on troubleshooting peak_nii. -Aaron On Tue, Oct 2, 2018 at 11:

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reporting exact, FDR corrected p-values for results obtained with GLMFlex/FIVE

I would follow up with Donald McLaren on troubleshooting peak_nii. -Aaron On Tue, Oct 2, 2018 at 11:

10/2/18

Isadora Olive, … Adam Teed7

8/23/18

post hoc invalid contrasts

Thank you for checking this out, Aaron. Your feedback helped me find that the code was only taking

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post hoc invalid contrasts

Thank you for checking this out, Aaron. Your feedback helped me find that the code was only taking

8/23/18

Olga Kurakova, Aaron Schultz2

8/20/18

Conjunction analysis and posthoc contrasts in GLM_Flex_Fast4

My guess is that there is something wrong with the data specification for the model. I would ensure

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Conjunction analysis and posthoc contrasts in GLM_Flex_Fast4

My guess is that there is something wrong with the data specification for the model. I would ensure

8/20/18

Nicolas Lori, Aaron Schultz2

8/20/18

Question about use of confounds in GLM_Flex_Fast4

Any variable can be added to the model to control for a confound. For instance x ~ y + age will

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Question about use of confounds in GLM_Flex_Fast4

Any variable can be added to the model to control for a confound. For instance x ~ y + age will

8/20/18

Fabio, Aaron Schultz2

8/20/18

posthoc contrasts from an interaction

Post-hocs can only be used to make simple comparisons, that is comparisons between two conditions or

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posthoc contrasts from an interaction

Post-hocs can only be used to make simple comparisons, that is comparisons between two conditions or

8/20/18

Meg Spriggs, … Aaron Schultz21

8/20/18

FIVE documentation

What was the nature of the error message? -Aaron On Friday, July 20, 2018 at 4:53:15 AM UTC-4,

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FIVE documentation

What was the nature of the error message? -Aaron On Friday, July 20, 2018 at 4:53:15 AM UTC-4,

8/20/18

Nicolas Lori, Aaron Schultz2

8/20/18

How to obtain the number of Voxels or Volume for each Cluster?

The VOI data structure will have information regarding the number of voxels in the cluster. The

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How to obtain the number of Voxels or Volume for each Cluster?

The VOI data structure will have information regarding the number of voxels in the cluster. The

8/20/18

7/26/18

Have a question about how to obtain number of Voxels or Volume for each Cluster by using FIVE?

Dear Aaron, Have a question about how to obtain number of Voxels or Volume for each Cluster by using

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Have a question about how to obtain number of Voxels or Volume for each Cluster by using FIVE?

Dear Aaron, Have a question about how to obtain number of Voxels or Volume for each Cluster by using

7/26/18

Harry Moore, Aaron Schultz36

7/12/18

spm_vol>spm_vol_hdr error, new user

Hi Aaron, Thanks, that has helped a lot! Regards Harry On 11 Jul 2018, at 17:36, Aaron Schultz <ap

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spm_vol>spm_vol_hdr error, new user

Hi Aaron, Thanks, that has helped a lot! Regards Harry On 11 Jul 2018, at 17:36, Aaron Schultz <ap

7/12/18

Pauline FAVRE, … Aaron Schultz27

7/10/18

error in FIVE/plotVOI

I guess the post hoc contrast plotting is buggier than I remember. I would suggest plotting from one

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error in FIVE/plotVOI

I guess the post hoc contrast plotting is buggier than I remember. I would suggest plotting from one

7/10/18

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