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DCAN-Labs / abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.
https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline
BSD 3-Clause "New" or "Revised" License
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Error in DCANBOLDProcessing #27

Closed MartinBa9210 closed 3 years ago

MartinBa9210 commented 4 years ago

Dear DCAN-staff, unfortunately I ran into an error at the BOLD processing stage of the pipeline. From here I can’t tell what this is about so I just copied the content of DCANBOLDProcessing_teardown.err

Subscript indices must either be real positive integers or logicals.

Error in sorter (line 11)

Error in analyses_v2 (line 27)

MATLAB:badsubscript Subscript indices must either be real positive integers or logicals.

Error in sorter (line 11)

Error in analyses_v2 (line 27)

MATLAB:badsubscript Subscript indices must either be real positive integers or logicals.

Error in sorter (line 11)

Error in analyses_v2 (line 27)

MATLAB:badsubscript

it's actually not happening to only a subset of the processed subjects, but all of them. So it seems something general isn't right here. Could you please have a look on your site, whats happening at those lines? Tell me if you need any additional information.

Thank you very much in advance and all the best, Martin

ericearl commented 4 years ago

@MartinBa9210 , What were the labels in your BIDS functional task-<label> runs and how were they numbered? I have seen something like this before, but I'm not certain what triggers it.

MartinBa9210 commented 4 years ago

Hey Eric, the naming was the following

sub-#ID_ses-1_task-RestingState_run-1_bold sub-#ID_ses-1_task-RestingState_run-2_bold sub-#ID_ses-1_task-FearTask_run-1_bold sub-#ID_ses-1_task-FoodTask_run-1_bold

same naming was used in the .json side car.

Best, Martin

ericearl commented 4 years ago

Thanks, @MartinBa9210 . Is that the input data naming or is that the names as they appear in the .../files/MNINonLinear/Results/ folder? I am very curious the names you have in that deeper processed data folder for those 4 task runs.

@perronea and @kathy-snider can we meet to speculate what might be going on here before Friday this week? Hit me up on Slack, please.

MartinBa9210 commented 4 years ago

Sorry, that's the naming of the input.

MNINonLinear is: task-RestingState1 task-RestingState2 task-FearTask1 task-FoodTask1

thanks for the quick response!

Best, Martin

perronea commented 4 years ago

@MartinBa9210 Can you email us (perronea@ohsu.edu and earl@ohsu.edu) the jsons located in ".../files/DCANBOLDProc_v4.0.0/analyses_v2/matlab_code" and include an ls of ".../files/MNINonLinear/Results". Please remove any subject ids if necessary. Thank you.

MartinBa9210 commented 4 years ago

Sure, I'll do that tomorrow... already left work.

Best, Martin

madisoth commented 3 years ago

This is a 15-month bump, but the source of the error in the original post is likely due to the two-digit run index assumption noted in this issue on the dcan_bold_processing repo: https://github.com/DCAN-Labs/dcan_bold_processing/issues/5

PR #39 updates the handling of session/task labels and run indices by both helpers.py and dcan_bold_processing, which is likely to resolve this issue.

MartinBa9210 commented 3 years ago

Alright, thank you for checking this! I’ll check that asap on my side.

If it works, 15 months wasn’t the problem, we’re still acquiring data and its easy to just do the last step.

Anyway, to my understanding the indices I’m using are in line with the guidelines of BIDS, right?!

Best, Martin

Am 06.08.2021 um 23:21 schrieb Thomas Madison @.***>:

This is a 15-month bump, but the source of the error in the original post is likely due to the two-digit run index assumption noted in this issue on the dcan_bold_processing repo: DCAN-Labs/dcan_bold_processing#5 https://github.com/DCAN-Labs/dcan_bold_processing/issues/5 PR #39 https://github.com/DCAN-Labs/abcd-hcp-pipeline/pull/39 updates the handling of session/task labels and run indices by both helpers.py and dcan_bold_processing, which is likely to resolve this issue.

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audreymhoughton commented 3 years ago

@MartinBa9210 I believe you are right about your indices technically being within the BIDS guidelines. Currently, this is one of those things that is specific to our pipeline.

kathy-snider commented 3 years ago

I believe this issue has been fixed with the latest version of dcan_bold_processing (v4.0.7). So pipelines that include that version should no longer have the problem. I tested this belief with the infant pipeline and it correctly processed runs with run_1 - run_12 (i.e., both 1 and 2 digit run numbers in the same session) with no problems.

arueter1 commented 3 years ago

Thanks Kathy!

Amanda

On Fri, Aug 13, 2021 at 3:29 PM Kathy @.***> wrote:

I believe this issue has been fixed with the latest version of dcan_bold_processing (v4.0.7). So pipelines that include that version should no longer have the problem. I tested this belief with the infant pipeline and it correctly processed runs with run_1 - run_12 (i.e., both 1 and 2 digit run numbers in the same session) with no problems.

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