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brainGraph-help

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kcampbell, Chris Watson2

May 14

mtpc edge-level data

I think it should be reasonable to apply MTPC to edge-level metrics. But I have not attempted it, and

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mtpc edge-level data

I think it should be reasonable to apply MTPC to edge-level metrics. But I have not attempted it, and

May 14

Jordi H, Chris Watson4

Apr 9

Question about NBS: which nodes are part of significant component?

I will just share my code here that I wrote (aka had ChatGPT write) to extract the components

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Question about NBS: which nodes are part of significant component?

I will just share my code here that I wrote (aka had ChatGPT write) to extract the components

Apr 9

Feb 22

Error in { : task 1 failed - "object 'NA' not found". I

Hi, Watson. When I was calculating random graphs controlling for clustering using the customized

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Error in { : task 1 failed - "object 'NA' not found". I

Hi, Watson. When I was calculating random graphs controlling for clustering using the customized

Feb 22

Jan 23

Question Regarding Lp Values in Random Graphs

Hi Chris, Thank you for creating such an amazing tool. I am currently working with your tools and

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Question Regarding Lp Values in Random Graphs

Hi Chris, Thank you for creating such an amazing tool. I am currently working with your tools and

Jan 23

Jonatan Ottino, … Hollie9

Jan 22

permutation testing in other metrics stored in dt.G

Hi both, I am also interested in computing graph level local efficiency and came across this thread.

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permutation testing in other metrics stored in dt.G

Hi both, I am also interested in computing graph level local efficiency and came across this thread.

Jan 22

8/1/24

Error in { : task 1 failed - "object 'NA' not found"

Hi everyone, I encountered an issue while using the NBS function in R. My code is as follows: nbs.

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Error in { : task 1 failed - "object 'NA' not found"

Hi everyone, I encountered an issue while using the NBS function in R. My code is as follows: nbs.

8/1/24

7/31/24

Clarifying Contrast and Alternative calls on NBS()

Following up on this. I have read the links on contrast coding attempting to apply it to NBS() to

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Clarifying Contrast and Alternative calls on NBS()

Following up on this. I have read the links on contrast coding attempting to apply it to NBS() to

7/31/24

IC K, … Chris Watson6

7/23/24

Error in apply(x, 3L, qr.default, ...) : 'MARGIN' does not match dim(X)

It works! Thank you so much. Chris Watson <chris.w...@gmail.com> 於 2024年6月22日週六上午1:15寫道：

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Error in apply(x, 3L, qr.default, ...) : 'MARGIN' does not match dim(X)

It works! Thank you so much. Chris Watson <chris.w...@gmail.com> 於 2024年6月22日週六上午1:15寫道：

7/23/24

7/5/24

mtpc analyses plots not showing null permutations at one specific threshold

(The second plot was local efficiency, hence the x axis label, sorry for the mistake. However exact

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mtpc analyses plots not showing null permutations at one specific threshold

(The second plot was local efficiency, hence the x axis label, sorry for the mistake. However exact

7/5/24

Sarah, … Hollie4

5/23/24

make_brainGraphList error message: "The `edges` argument of `as_adjacency_matrix()` was deprecated in igraph 2.0.0 and is now defunct."

This worked perfectly - thanks so much Lionel!! On Thursday 16 May 2024 at 01:07:38 UTC+10 Lionel

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make_brainGraphList error message: "The `edges` argument of `as_adjacency_matrix()` was deprecated in igraph 2.0.0 and is now defunct."

This worked perfectly - thanks so much Lionel!! On Thursday 16 May 2024 at 01:07:38 UTC+10 Lionel

5/23/24

Chris Watson, J4

2/23/24

Re: [brainGraph-help] All atlas in braingraph has even numbers of the areas, and it's effect on the custom atlas.

I found the solution after several trial-and-error experiemnts : ) the 'B' is used at certain

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Re: [brainGraph-help] All atlas in braingraph has even numbers of the areas, and it's effect on the custom atlas.

I found the solution after several trial-and-error experiemnts : ) the 'B' is used at certain

2/23/24

y li, Chris Watson2

8/9/23

brain network communication models

I didn't write code for those and, if I do in the future, it won't be for quite awhile. I

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brain network communication models

I didn't write code for those and, if I do in the future, it won't be for quite awhile. I

8/9/23

virva.sa...@gmail.com, Chris Watson2

8/9/23

get.resid error

Please read the User Guide to understand the purpose of "get.resid". You can probably do

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get.resid error

Please read the User Guide to understand the purpose of "get.resid". You can probably do

8/9/23

danandre...@gmail.com, Chris Watson4

3/25/23

Custom atlas trouble in make_brainGraphList, v3.0.2, windows, R version 4.2.1

Sorry for such a long delay, but I didn't get the same error "Schaefer_atlas not found"

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Custom atlas trouble in make_brainGraphList, v3.0.2, windows, R version 4.2.1

Sorry for such a long delay, but I didn't get the same error "Schaefer_atlas not found"

3/25/23

Anthony Juliano, Chris Watson2

3/25/23

make_brainGraphList error message: "'x' must be an array of at least two dimensions"

Are you getting the same error for high thresholds? Sometimes that error occurs on more sparse graphs

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make_brainGraphList error message: "'x' must be an array of at least two dimensions"

Are you getting the same error for high thresholds? Sometimes that error occurs on more sparse graphs

3/25/23

Jake Powell, Chris Watson2

3/15/23

Weighted Assortativity

No, you'd have to write our own function or find one in some other package to calculate weighted

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Weighted Assortativity

No, you'd have to write our own function or find one in some other package to calculate weighted

3/15/23

Melanie Ehrler2

2/22/23

error during make_brainGraphList()

here is a subset of the data Melanie Ehrler schrieb am Dienstag, 21. Februar 2023 um 18:16:39 UTC+1:

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error during make_brainGraphList()

here is a subset of the data Melanie Ehrler schrieb am Dienstag, 21. Februar 2023 um 18:16:39 UTC+1:

2/22/23

Todd Richards, Chris Watson3

11/28/22

error message during execution

Okay, I was able to get this command to work without parallel processing g.tmp <-

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error message during execution

Okay, I was able to get this command to work without parallel processing g.tmp <-

11/28/22

Hui Xu, Chris Watson2

11/28/22

object 'new.order' not found when plotting adjacency matrix

Hi Hui, sorry for the long delay in response. If this error still occurs for you, please follow the

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object 'new.order' not found when plotting adjacency matrix

Hi Hui, sorry for the long delay in response. If this error still occurs for you, please follow the

11/28/22

Sara Bock, Chris Watson2

11/28/22

Error when trying to get residuals

I'm sorry for such a long delay in replying. If this is still a problem, I would need the actual

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Error when trying to get residuals

I'm sorry for such a long delay in replying. If this is still a problem, I would need the actual

11/28/22

mariaeugeni...@gmail.com, … Chris Watson26

11/28/22

error from make_brainGraphList

I apologize for such a long delay; I hadn't been able to devote time to the package. But I will

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error from make_brainGraphList

I apologize for such a long delay; I hadn't been able to devote time to the package. But I will

11/28/22

Hui Xu, Chris Watson4

4/19/22

How to get a graph for each subject

Hi Chirs, Thank you so much for your reply. It's my first time using brainGraph to perform

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How to get a graph for each subject

Hi Chirs, Thank you so much for your reply. It's my first time using brainGraph to perform

4/19/22

jonata...@gmail.com, Chris Watson6

12/1/21

SCN pipeline – using custom atlas for DTI

Actually you could also pass the "atlas" argument when calling "get.resid", and

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SCN pipeline – using custom atlas for DTI

Actually you could also pass the "atlas" argument when calling "get.resid", and

12/1/21

Alice Ballerini, Chris Watson8

11/25/21

Error in vapply

I believe the function (invisibly) outputs a list object with a data.table. So you should be able to

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Error in vapply

I believe the function (invisibly) outputs a list object with a data.table. So you should be able to

11/25/21

Lei Guo, … Alice Ballerini6

10/7/21

Data import through import_scn for structural covariance network

Hi Chris, I solved the error by modifying the code string in "import.R" file, now it works.

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Data import through import_scn for structural covariance network

Hi Chris, I solved the error by modifying the code string in "import.R" file, now it works.

10/7/21

Gershon Spitz, Chris Watson3

9/1/21

"Object NA" error when control for clustering

Hi Chris, Thank you for the reply. I amended the function but still received the same error message.

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"Object NA" error when control for clustering

Hi Chris, Thank you for the reply. I amended the function but still received the same error message.

9/1/21

virva.sa...@gmail.com, Chris Watson6

8/18/21

I defined the function as you instructed and now the code seems to work. Thank you so much for your

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I defined the function as you instructed and now the code seems to work. Thank you so much for your

8/18/21

Gershon Spitz, … Chris Watson10

8/5/21

Error during make_brainGraphList

Perfect! Thanks Chris. Changing within_module_deg_z_score worked. Best wishes, Gershon. On Thu, 5 Aug

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Error during make_brainGraphList

Perfect! Thanks Chris. Changing within_module_deg_z_score worked. Best wishes, Gershon. On Thu, 5 Aug

8/5/21

kcampbell, Chris Watson3

7/7/21

Matrix Normalization in create_mats

Thanks for your quick response! I was able to access "normalize_mats" with: > View(

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Matrix Normalization in create_mats

Thanks for your quick response! I was able to access "normalize_mats" with: > View(

7/7/21

jonata...@gmail.com, … kcampbell8

6/22/21

make_brainGraphList error when thrs.by = 'consensus'

Hi Chirs, My apologies, it turns out I made an error in one of the thresholds I specified, which

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make_brainGraphList error when thrs.by = 'consensus'

Hi Chirs, My apologies, it turns out I made an error in one of the thresholds I specified, which

6/22/21

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