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CBIG users

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Welcome to CBIG user group. You will be notified about major updates & bugs involving the CBIG GitHub repository (https://github.com/ThomasYeoLab/CBIG). You are also welcomed to post questions and issues in this group.

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Jan 4

Re: [cbig_users] The script CBIG_preproc_fMRI_preprocess.csh failed to generate the file md1001_bld000_FDRMS0.2_DVARS50_motion_outliers.txt, resulting in an error.

Hi Yaoyao, Could you please provide us with more details about this issue? Or it might be a bit

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Re: [cbig_users] The script CBIG_preproc_fMRI_preprocess.csh failed to generate the file md1001_bld000_FDRMS0.2_DVARS50_motion_outliers.txt, resulting in an error.

Hi Yaoyao, Could you please provide us with more details about this issue? Or it might be a bit

Jan 4

Boletu Peng, Ruby Kong3

Jan 3

Request for MEX Source Code to Develop Standalone/Accelerated Version of MS-HBM

Dear Ruby, Thank you so much for your prompt response and for sharing the source files! We truly

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Request for MEX Source Code to Develop Standalone/Accelerated Version of MS-HBM

Dear Ruby, Thank you so much for your prompt response and for sharing the source files! We truly

Jan 3

kianal...@gmail.com, Thomas Yeo3

12/29/25

Individualized Subcortical Parcellations/Segementations?

Hello Thomas, Thank you for the helpful recommendation! I have a brief follow-up question. For the

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Individualized Subcortical Parcellations/Segementations?

Hello Thomas, Thank you for the helpful recommendation! I have a brief follow-up question. For the

12/29/25

kianal...@gmail.com, Aihuiping Xue3

12/18/25

Preprocessing for Kong 2022 areal-level MS-HBM pipeline

I ran the deoblique step within an AFNI container first, and was able to run all the rest the steps

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Preprocessing for Kong 2022 areal-level MS-HBM pipeline

I ran the deoblique step within an AFNI container first, and was able to run all the rest the steps

12/18/25

Patrick Sadil, Thomas Yeo2

10/29/25

Availability of FD, DVARS, or Censored Frames in HCP YA for replicating Ooi et al. 2025?

Hi Patrick, Leon told me has responded to you, so I will assume this issue is resolved. Feel free to

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Availability of FD, DVARS, or Censored Frames in HCP YA for replicating Ooi et al. 2025?

Hi Patrick, Leon told me has responded to you, so I will assume this issue is resolved. Feel free to

10/29/25

Patrick Sadil, Leon Ooi3

10/27/25

Ooi et al. 2025 - Availability of HCP correlation results?

I see those now. Thanks! On Friday, October 24, 2025 at 7:56:05 PM UTC-4 Leon Ooi wrote: Hi Patrick,

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Ooi et al. 2025 - Availability of HCP correlation results?

I see those now. Thanks! On Friday, October 24, 2025 at 7:56:05 PM UTC-4 Leon Ooi wrote: Hi Patrick,

10/27/25

Simone Cauzzo, … Thomas Yeo7

10/8/25

LUT conversion from volumetric Schaefer 2018 to yeo7 surface FS parcel

Oh, this makes things clearer. Thank you both for the help, I understand that there is no mapping

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LUT conversion from volumetric Schaefer 2018 to yeo7 surface FS parcel

Oh, this makes things clearer. Thank you both for the help, I understand that there is no mapping

10/8/25

Ana Radanovic, Shaoshi Zhang10

9/2/25

Zhang 2024 pFIC model unable to simulate empirical CDF

Glad to hear it's resolved! Always happy to help. Shaoshi On Wednesday, 3 September 2025 at 7:30:

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Zhang 2024 pFIC model unable to simulate empirical CDF

Glad to hear it's resolved! Always happy to help. Shaoshi On Wednesday, 3 September 2025 at 7:30:

9/2/25

Melissa, … Thomas Yeo7

8/18/25

low homogeneity in MS-HBM network recovery

Hi Melissa, It does look weird. For example, you seem to have separate visual networks on the left

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low homogeneity in MS-HBM network recovery

Hi Melissa, It does look weird. For example, you seem to have separate visual networks on the left

8/18/25

Christophe Tanguay Sabourin

7/21/25

Re: [cbig_users] Digest for cbig_users@googlegroups.com - 1 update in 1 topic

Please unsuscribe me from the list. Thank you From: cbig_...@googlegroups.com <cbig_users@

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Re: [cbig_users] Digest for cbig_users@googlegroups.com - 1 update in 1 topic

Please unsuscribe me from the list. Thank you From: cbig_...@googlegroups.com <cbig_users@

7/21/25

Ruyi Pan, Ruby Kong2

7/17/25

Kong 2022 Areal_level MS-HBM pipeline: generate the gradient prior error

Hi Ruyi, I think this error happens for newer Matlab version it doesn't allow for duplicate edges

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Kong 2022 Areal_level MS-HBM pipeline: generate the gradient prior error

Hi Ruyi, I think this error happens for newer Matlab version it doesn't allow for duplicate edges

7/17/25

6/27/25

Update of Meta Matching Models Repository

Dear CBIG users, Recently we found that in meta-matching with stacking, not normalizing y (labels)

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Update of Meta Matching Models Repository

Dear CBIG users, Recently we found that in meta-matching with stacking, not normalizing y (labels)

6/27/25

Yuchen Liu, Shreya Pande3

4/1/25

Yeo et al., 2011 Network Lookup Table Color Confirmation

Dear Shreya, Thank you very much for your kind reply! I used the LUT file as you suggested with the

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Yeo et al., 2011 Network Lookup Table Color Confirmation

Dear Shreya, Thank you very much for your kind reply! I used the LUT file as you suggested with the

4/1/25

Saiwen Yu, Thomas Yeo2

3/21/25

how to deal with Schaefer 2018 fsLR 1000 n missing data points?

Hi Saiwen, Can you elaborate a little more? The Schaefer parcellation was generated in fsaverage6

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how to deal with Schaefer 2018 fsLR 1000 n missing data points?

Hi Saiwen, Can you elaborate a little more? The Schaefer parcellation was generated in fsaverage6

3/21/25

Edward Zuniga, Aihuiping Xue6

3/17/25

Installing CBIG Repository on Rocky Linux 8

Great, thank you! On Sun, Mar 16, 2025 at 10:31 PM Aihuiping Xue <xueaih...@gmail.com> wrote

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Installing CBIG Repository on Rocky Linux 8

Great, thank you! On Sun, Mar 16, 2025 at 10:31 PM Aihuiping Xue <xueaih...@gmail.com> wrote

3/17/25

3/17/25

Important Update: Bug Fix in CBIG_preproc_fslmcflirt_outliers for multi-echo cases

Dear CBIG Repository Users, We would like to bring your attention to a recently identified bug in the

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Important Update: Bug Fix in CBIG_preproc_fslmcflirt_outliers for multi-echo cases

Dear CBIG Repository Users, We would like to bring your attention to a recently identified bug in the

3/17/25

Gin Cruz, Thomas Yeo3

2/9/25

Yan 2023 parcellation atlas

Thank you, Thomas. My second question has been resolved -- I incorrectly loaded the files to

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Yan 2023 parcellation atlas

Thank you, Thomas. My second question has been resolved -- I incorrectly loaded the files to

2/9/25

Arpana Annie Gupta

10/24/24

Open Postdoc Positions at UCLA

Looking for highly motivated and talented postdocs to work in a dynamic translational and cutting

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Open Postdoc Positions at UCLA

Looking for highly motivated and talented postdocs to work in a dynamic translational and cutting

10/24/24

Thomas Yeo, Alexander Cohen2

10/24/24

calculator for exploring scan time and sample size

This is great! - Alex ——————————————— Permanent email: alex...@gmail.com Science/Medical email:

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calculator for exploring scan time and sample size

This is great! - Alex ——————————————— Permanent email: alex...@gmail.com Science/Medical email:

10/24/24

lorenzo pasquini, Ruby Kong15

10/9/24

MSHBM implementation in clinical trial: potential collaboration with UCSF

Just another quick note. For Schaefer atlases we have different versions. They are actually the same

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MSHBM implementation in clinical trial: potential collaboration with UCSF

Just another quick note. For Schaefer atlases we have different versions. They are actually the same

10/9/24

Yijun Liu, Aihuiping Xue2

9/2/24

script to map from fsaverage 6 to fs_LR 32K space

Hi Yijun, Please check https://github.com/ThomasYeoLab/CBIG/blob/master/utilities/matlab/fslr_matlab/

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script to map from fsaverage 6 to fs_LR 32K space

Hi Yijun, Please check https://github.com/ThomasYeoLab/CBIG/blob/master/utilities/matlab/fslr_matlab/

9/2/24

abid.y....@gmail.com

8/19/24

minor bug in CBIG_preproc_convert_input_BIDS.csh

Hi Yan Hongwei, When I put in: $CBIG_CODE_DIR/stable_projects/preprocessing/CBIG_fMRI_Preproc2016/

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minor bug in CBIG_preproc_convert_input_BIDS.csh

Hi Yan Hongwei, When I put in: $CBIG_CODE_DIR/stable_projects/preprocessing/CBIG_fMRI_Preproc2016/

8/19/24

lorenzo pasquini, Ruby Kong6

7/23/24

Invalid MEX-file simplified Kong 2022 parcellation

Thanks Ruby, I moved on to use the scripts on linux and things have been smoother. Could I ask you

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Invalid MEX-file simplified Kong 2022 parcellation

Thanks Ruby, I moved on to use the scripts on linux and things have been smoother. Could I ask you

7/23/24

Howie Qu, Thomas Yeo2

5/27/24

Schaefer atlas anatomical network parcellation?

Hi Shijie, Sorry we don't have that. Regards, Thomas On Tue, May 28, 2024 at 12:14 AM Howie Qu

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Schaefer atlas anatomical network parcellation?

Hi Shijie, Sorry we don't have that. Regards, Thomas On Tue, May 28, 2024 at 12:14 AM Howie Qu

5/27/24

Yijun Liu, yanhongwei_a4

5/13/24

load preprocessed fMRI in fsaverage6 space in matlab

Hi Hongwei, Thanks a lot for your detailed explanation! Yijun On Sun, May 12, 2024 at 7:35 PM '

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load preprocessed fMRI in fsaverage6 space in matlab

Hi Hongwei, Thanks a lot for your detailed explanation! Yijun On Sun, May 12, 2024 at 7:35 PM '

5/13/24

Yunhong Wang, Thomas Yeo2

5/6/24

Extract morphometric index from T1 and DWI using Schefer400 atlas

Hi Yunhong, If you have the Schaefer parcellation annot for individual participants AND you have the

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Extract morphometric index from T1 and DWI using Schefer400 atlas

Hi Yunhong, If you have the Schaefer parcellation annot for individual participants AND you have the

5/6/24

Yijun Liu, Aihuiping Xue7

4/24/24

Preprocessing config of GSP dataset used in Yan et al., 2023 & Li et al., 2019

Hi Aihuiping, Thanks for your reply! Yijun On Wed, Apr 24, 2024 at 12:10 AM Aihuiping Xue <

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Preprocessing config of GSP dataset used in Yan et al., 2023 & Li et al., 2019

Hi Aihuiping, Thanks for your reply! Yijun On Wed, Apr 24, 2024 at 12:10 AM Aihuiping Xue <

4/24/24

Yunhong Wang, Thomas Yeo3

4/15/24

The process of training Gaussian classifer surface atlas of Schaefer 2018

Hi Yunhong, Oh! I see. Yes, you are right we did create a Gaussian classifier at some point. I stand

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The process of training Gaussian classifer surface atlas of Schaefer 2018

Hi Yunhong, Oh! I see. Yes, you are right we did create a Gaussian classifier at some point. I stand

4/15/24

Know ledge, Thomas Yeo2

3/18/24

Subcortical Brain regions in the 7/17 network (Yeo et al., 2011)

Hi Yuchen, The Yeo2011 parcellation is a cortical parcellation. For subcortical, you can consider our

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Subcortical Brain regions in the 7/17 network (Yeo et al., 2011)

Hi Yuchen, The Yeo2011 parcellation is a cortical parcellation. For subcortical, you can consider our

3/18/24

Ziteng Han, … Xiaoxuan10

10/31/23

Replicating the Schafer brain parcellation project

Dear CBIG community, I'd like to ask two further questions if you don't mind. When I ran

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Replicating the Schafer brain parcellation project

Dear CBIG community, I'd like to ask two further questions if you don't mind. When I ran

10/31/23

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