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DCAN-Labs / dcan_bold_processing

functional connectivity preprocessing for resting state fMRI outputs of the dcan-fmri-pipelines
BSD 3-Clause "New" or "Revised" License
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truncating data #24

Closed jkkenley closed 9 months ago

jkkenley commented 1 year ago

I am using docker version: dcanlabs/abcd-hcp-pipeline:v0.0.3

When I run the docker I see the following screen output: raceback (most recent call last): File "/app/run.py", line 364, in _cli() File "/app/run.py", line 67, in _cli return interface(**kwargs) File "/app/run.py", line 360, in interface stage.run(ncpus) File "/app/pipelines.py", line 588, in run self.teardown(result) File "/app/pipelines.py", line 534, in teardown self.class.name) Exception: error caught during stage: FMRIVolume

The log files within the FMRIVolume folder indicate the error is: json: "stage erminated with exit code [0, 1, 1, 0]" .err: ERROR (nifti_image_read): short header read '/output/sub-test1/ses-None/files/task-rest02/task-rest02_gdc.nii.gz' ERROR: nifti_image_open(/output/sub-test1/ses-None/files/task-rest02/task-rest02_gdc): bad header info ERROR: failed to open file /output/sub-test1/ses-None/files/task-rest02/task-rest02_gdc Cannot open volume /output/sub-test1/ses-None/files/task-rest02/task-rest02_gdc for reading!

When I review these files they have been truncated down from there original size from 383 frames to 233 and I don't know why.

Thank you for your help. Jeanette

lundq163 commented 1 year ago

Hi Jeanette, I would recommend using this docker version: dcanumn/abcd-hcp-pipeline:v0.1.3 Please update this thread if you continue running into the same error, thanks!

jkkenley commented 1 year ago

Thank you! I'll try that!

Am I correct in understanding this is latest version?

Thanks, Jeanette

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From: lundq163 @.> Sent: Monday, April 24, 2023 2:09 PM To: DCAN-Labs/dcan_bold_processing @.> Cc: Kenley, Jeanette @.>; Author @.> Subject: Re: [DCAN-Labs/dcan_bold_processing] truncating data (Issue #24)

Hi Jeanette, I would recommend using this docker version: dcanumn/abcd-hcp-pipeline:v0.1.3 Please update this thread if you continue running into the same error, thanks!

— Reply to this email directly, view it on GitHubhttps://github.com/DCAN-Labs/dcan_bold_processing/issues/24#issuecomment-1520688571, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUYL7WTTV7EVLV6556S2G7LXC3FYBANCNFSM6AAAAAAXJSWFKY. You are receiving this because you authored the thread.Message ID: @.***>

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lundq163 commented 1 year ago

correct

jkkenley commented 1 year ago

Thanks!

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From: lundq163 @.> Sent: Monday, April 24, 2023 3:49 PM To: DCAN-Labs/dcan_bold_processing @.> Cc: Kenley, Jeanette @.>; Author @.> Subject: Re: [DCAN-Labs/dcan_bold_processing] truncating data (Issue #24)

correct

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jkkenley commented 1 year ago

That worked!

Thanks for much!

Does the docker have anything like the below which could be used as a QC measure for registration of the bold after distortion correction? [cid:5abbf5fc-7b22-4074-b6d1-dcb1e5148157]

Is this file the closest?

[cid:c1bdeb66-7c27-45aa-bd59-21d92eaf7ab7]

The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

From: Kenley, Jeanette @.> Sent: Monday, April 24, 2023 2:57 PM To: DCAN-Labs/dcan_bold_processing @.>; DCAN-Labs/dcan_bold_processing @.> Cc: Author @.> Subject: Re: [DCAN-Labs/dcan_bold_processing] truncating data (Issue #24)

Thank you! I'll try that!

Am I correct in understanding this is latest version?

Thanks, Jeanette

The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

From: lundq163 @.> Sent: Monday, April 24, 2023 2:09 PM To: DCAN-Labs/dcan_bold_processing @.> Cc: Kenley, Jeanette @.>; Author @.> Subject: Re: [DCAN-Labs/dcan_bold_processing] truncating data (Issue #24)

Hi Jeanette, I would recommend using this docker version: dcanumn/abcd-hcp-pipeline:v0.1.3 Please update this thread if you continue running into the same error, thanks!

— Reply to this email directly, view it on GitHubhttps://github.com/DCAN-Labs/dcan_bold_processing/issues/24#issuecomment-1520688571, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUYL7WTTV7EVLV6556S2G7LXC3FYBANCNFSM6AAAAAAXJSWFKY. You are receiving this because you authored the thread.Message ID: @.***>

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

audreymhoughton commented 11 months ago

@jkkenley we cannot see the images you have attached because you are responding via email. Can you respond via github with the images you attached so we can understand what you are asking?

lundq163 commented 9 months ago

@jkkenley, I am going to close this issue for now. Please respond whenever if you feel like you still need any assistance