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This is a forum to discuss issues related to the Configurable Pipeline for the Analysis of Connectomes software system. Feel free to use this mailing list to ask CPAC related questions and bug reports. We will do our best to respond in a timely manner.

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Mounami Kayitha, Amy Gutierrez2

3/3/23

CPAC: TypeError: Input nifti fie is not a 4D file

Hello, Thanks for reaching out! If there were any crash files, can you attach them? Can you also

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CPAC: TypeError: Input nifti fie is not a 4D file

Hello, Thanks for reaching out! If there were any crash files, can you attach them? Can you also

3/3/23

Mounami Kayitha, sgia...@gmail.com3

2/22/23

How to run CPAC processing using fMRIPrep preprocessed outputs

Thank you so much for responding! At the moment, I am trying to run time series extraction on the

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How to run CPAC processing using fMRIPrep preprocessed outputs

Thank you so much for responding! At the moment, I am trying to run time series extraction on the

2/22/23

彌富泰佑, Jon Clucas, MIS14

2/15/23

Question about lFCD calculation with CPAC

Dear Jon, Thank you so much for your wonderful advice. I am sorry for my terribly delayed response.

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Question about lFCD calculation with CPAC

Dear Jon, Thank you so much for your wonderful advice. I am sorry for my terribly delayed response.

2/15/23

Francesco Molla, Amy Gutierrez7

10/4/22

Error calling FSL-BET

Additionally, you can also change your FSLDIR in your pipeline_file.yml (line 140) to FSLDIR (example

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Error calling FSL-BET

Additionally, you can also change your FSLDIR in your pipeline_file.yml (line 140) to FSLDIR (example

10/4/22

Joshua Lee, sgia...@gmail.com3

10/3/22

Is this the cpac forum still?

Also I see you posted on our GitHub Issues page- if this is the issue you're experiencing we can

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Is this the cpac forum still?

Also I see you posted on our GitHub Issues page- if this is the issue you're experiencing we can

10/3/22

사회과학대학/박수진

7/12/22

run cwas pipeline with cpac with already preprocessed fMRI data

Hi, cpac experts! I am so relieved to find this forum and want to ask a few questions. I am trying to

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run cwas pipeline with cpac with already preprocessed fMRI data

Hi, cpac experts! I am so relieved to find this forum and want to ask a few questions. I am trying to

7/12/22

Xiaochen TANG, sgia...@gmail.com2

7/7/22

Error in building group config file by "cpac group feat load_preset"

Hello Xiaochen, The CPAC group model builder is currently considered deprecated - we've moved

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Error in building group config file by "cpac group feat load_preset"

Hello Xiaochen, The CPAC group model builder is currently considered deprecated - we've moved

7/7/22

Francesco Molla, Jon Clucas, MIS12

3/29/22

nhp-macaque pipeline

Hi Jon, I think I found out what went wrong by re-running the pipeline from scratch and deleting the

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nhp-macaque pipeline

Hi Jon, I think I found out what went wrong by re-running the pipeline from scratch and deleting the

3/29/22

이지원, Jon Clucas, MIS15

3/14/22

Hi, Jon Clucas ! Thanks for helping me understand. In preprocessing steps (https://fcp-indi.github.io

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Hi, Jon Clucas ! Thanks for helping me understand. In preprocessing steps (https://fcp-indi.github.io

3/14/22

Xin Niu, Jon Clucas, MIS4

3/14/22

how to run cpac after configure the data_setttings.yml and data_config.yml?

I tried: docker run -i --rm --user $(id -u):$(id -g) \ -v $dataPath:$dataPath \ -v $outputPath:$

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how to run cpac after configure the data_setttings.yml and data_config.yml?

I tried: docker run -i --rm --user $(id -u):$(id -g) \ -v $dataPath:$dataPath \ -v $outputPath:$

3/14/22

FEDERICO CAMPO, Jon Clucas, MIS6

3/11/22

Atlases for timeseries extraction

Hi John Cluas, Thank you so much for your explanation. Now it's all more clear to me. Kind

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Atlases for timeseries extraction

Hi John Cluas, Thank you so much for your explanation. Now it's all more clear to me. Kind

3/11/22

이지원, Jon Clucas, MIS8

2/8/22

Error on data_setting.yml

Hi Jon Clucas, Now, I understood all. Thank you for your friendly reply. Thanks, LEE 2022년 2월 2일 수요일

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Error on data_setting.yml

Hi Jon Clucas, Now, I understood all. Thank you for your friendly reply. Thanks, LEE 2022년 2월 2일 수요일

2/8/22

Federico, … Jon Clucas, MIS5

1/28/22

Running C-PAC pipeline on ABIDE dataset

Hi Federico, I'm sorry I wasn't clearer ― I didn't intend to suggest to use Docker

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Running C-PAC pipeline on ABIDE dataset

Hi Federico, I'm sorry I wasn't clearer ― I didn't intend to suggest to use Docker

1/28/22

1/24/22

Re: cpac run ERROR

Hi Lee, Thank you for reaching out to us. Could you send us the crash files in the log directory?

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Re: cpac run ERROR

Hi Lee, Thank you for reaching out to us. Could you send us the crash files in the log directory?

1/24/22

TT, Jon Clucas, MIS5

8/25/21

CPAC 1.8.0 fALFF maps output issue

Hi Alex, Thanks for continuing to dig in. A couple other team members have been looking into this

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CPAC 1.8.0 fALFF maps output issue

Hi Alex, Thanks for continuing to dig in. A couple other team members have been looking into this

8/25/21

7/15/21

default pipeline from "design a pipeline" configurable pipeline option

Hello, If I design a pipeline at "https://fcp-indi.github.io/C-PAC_GUI/" the default

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default pipeline from "design a pipeline" configurable pipeline option

Hello, If I design a pipeline at "https://fcp-indi.github.io/C-PAC_GUI/" the default

7/15/21

Moyan Li, Jon Clucas, MIS16

6/23/21

run data_setting.yml

Hi Jon, Yes, all of my attempts have all been for the same subject. As you said, it's still

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run data_setting.yml

Hi Jon, Yes, all of my attempts have all been for the same subject. As you said, it's still

6/23/21

Moyan Li, Jon Clucas2

6/22/21

Procedure stuck when running slice_timing

Hi Moyan, See response 1 here. Based on the callback log in that thread, I'd estimate slice

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Procedure stuck when running slice_timing

Hi Moyan, See response 1 here. Based on the callback log in that thread, I'd estimate slice

6/22/21

Moyan Li, sgia...@gmail.com3

6/21/21

Select my pipeline with FALFF

Hi Steve, Thanks for your explanation. I see your point. I am wondering if I could just get ALFF and

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Select my pipeline with FALFF

Hi Steve, Thanks for your explanation. I see your point. I am wondering if I could just get ALFF and

6/21/21

mkim, sgia...@gmail.com2

6/21/21

Hello, M-SDB means all 3 (delayed, squared, and delayed+squared). A quick note: C-PAC v1.8+ allows

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Hello, M-SDB means all 3 (delayed, squared, and delayed+squared). A quick note: C-PAC v1.8+ allows

6/21/21

TT, sgia...@gmail.com2

6/21/21

Motion scrubbing in C-PAC 1.8.0

Hi Alex, It is indeed still in C-PAC. The nuisance regression suite has been expanded and the naming

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Motion scrubbing in C-PAC 1.8.0

Hi Alex, It is indeed still in C-PAC. The nuisance regression suite has been expanded and the naming

6/21/21

6/17/21

Is there a problem with nuisance regression or registration?

Hello, I am a newbie in preprocessing and fMRI analysis. I tried to set up a preprocessing pipeline

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Is there a problem with nuisance regression or registration?

Hello, I am a newbie in preprocessing and fMRI analysis. I tried to set up a preprocessing pipeline

6/17/21

Ryan Wales, sgia...@gmail.com2

5/26/21

Analyzing data preprocessed elsewhere

Hi Ryan, This is now possible with C-PAC. It's a very new addition, and we're currently

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Analyzing data preprocessed elsewhere

Hi Ryan, This is now possible with C-PAC. It's a very new addition, and we're currently

5/26/21

Óscar Peña-Nogales, sgia...@gmail.com2

5/26/21

Hi Oscar, There are many different ways to go about calculating a connectome that are too numerous

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Hi Oscar, There are many different ways to go about calculating a connectome that are too numerous

5/26/21

Ryan Wales, Jon Clucas, MIS2

4/29/21

Running on singularity syntax

Hi Ryan, Thanks for reaching out with your questions. Lines 2 ‒ 4 Lines 2 ‒ 4 are telling Singularity

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Running on singularity syntax

Hi Ryan, Thanks for reaching out with your questions. Lines 2 ‒ 4 Lines 2 ‒ 4 are telling Singularity

4/29/21

Óscar Peña-Nogales, sgia...@gmail.com4

4/1/21

fMRI, ALFF, ReHo Maps validation

Hi Óscar, Ah I see - yes, I have several friends/colleagues in the DWI world and I've seen the

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fMRI, ALFF, ReHo Maps validation

Hi Óscar, Ah I see - yes, I have several friends/colleagues in the DWI world and I've seen the

4/1/21

Annika Mayer, Jon Clucas, MIS9

3/22/21

C-PAC v.1.6.2 SameFile Error and time point missmatch error

Hi Annika, We recently released C-PAC v1.8.0. If you're still trying to use C-PAC and

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C-PAC v.1.6.2 SameFile Error and time point missmatch error

Hi Annika, We recently released C-PAC v1.8.0. If you're still trying to use C-PAC and

3/22/21

Erick Zhou, sgia...@gmail.com3

1/8/21

How to use the publicly shared fMRI data processed by C-PAC pipeline?

Dear Mr. Steven Giavasis, I am very grateful for your answer I have waited for a month to get answers

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How to use the publicly shared fMRI data processed by C-PAC pipeline?

Dear Mr. Steven Giavasis, I am very grateful for your answer I have waited for a month to get answers

1/8/21

Erick Zhou, Cameron Craddock2

12/16/20

Do I need to strip off all the additional planes of zeros before matching the fMRI data and the atlas?

Hello Zhongxing, I sent a reply to another of your emails. Strictly speaking this is not the correct

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Do I need to strip off all the additional planes of zeros before matching the fMRI data and the atlas?

Hello Zhongxing, I sent a reply to another of your emails. Strictly speaking this is not the correct

12/16/20

victorp...@gmail.com, sgia...@gmail.com3

11/15/20

Software versions in CPAC v1.6.2.a

Thank you very much, Steve! I didn't find the AFNI and FSL versions there, but I found them

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Software versions in CPAC v1.6.2.a

Thank you very much, Steve! I didn't find the AFNI and FSL versions there, but I found them

11/15/20

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