Closed MartinBa9210 closed 3 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.
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
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.
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
@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.
Sure, I'll do that tomorrow... already left work.
Best, Martin
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.
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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@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.
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.
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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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