regex changes, fixes for abcd-hcp-pipeline + nhp-abcd-bids-pipeline

madisoth commented 3 years ago

fix issues related to changes in get_fmriname function in helpers.py of DCAN pipeline BIDS-Apps (ideally get_fmriname in macaque and abcd-hcp pipeline will be updated to be consistent w/ infant pipeline going forward)
session/task regexes changed to be consistent with get_fmriname in infant pipeline
add --legacy-tasknames flag to parse input tasknames consistent with versions <= 4.0.4; may be needed for older HCP-style input e.g. "task-myTask01"(as opposed to BIDS-style "task-myTask_run-01")
use -legacy-mode flag with -cifti-parcellate to keep behavior consistent with wb_command < 1.4.0 / avoid error when concatenated timeseries has empty grayordinates
fix unfiltered motion tsv writeout
fix sorter.m error on tasks without run index
may also resolve #5 , but has not been tested on actual fMRIPrep output yet
compiled with R2017a / v9.2 MCC (same as current release)

arueter1 commented 3 years ago

@madisoth Can you make the 1 little change that Kathy suggested and then I will approve it and merge. :) Thanks!

madisoth commented 3 years ago

@kathy-snider I agree with your suggestion, I will get it added! The one drawback is that it's going to take extra work to accommodate both run indices of arbitrary length and task names ending in digits; e.g. does "ses-mySes-task-T0001.dtseries.nii" mean:

task=T, run=0001 task=T00 run=01 task=T0001, run=n/a
?

so for now I'll just add your suggested fix, and disclaimer that task names ending in digits won't be supported.

kathy-snider commented 3 years ago

This would only affect the BIDS version, i.e., non-legacy. So you could have task-rest_run-1 or task-rest_run-000001 and the "+" would get all of the digits whereas the {2,} only gets the digits on the second one (run-000001), but would not match the first one (run-1).

From: Thomas Madison @.***> Sent: Wednesday, August 4, 2021 11:03 AM To: DCAN-Labs/dcan_bold_processing Cc: Kathy Snider; Mention Subject: [EXTERNAL] Re: [DCAN-Labs/dcan_bold_processing] regex changes, fixes for abcd-hcp-pipeline + nhp-abcd-bids-pipeline (#15)

@kathy-sniderhttps://github.com/kathy-snider I agree with your suggestion, I will get it added! The one drawback is that it's going to take extra work to accommodate both run indices of arbitrary length and task names ending in digits; e.g. does "ses-mySes-task-T0001.dtseries.nii" mean:

task=T, run=0001 task=T00 run=01 task=T0001, run=n/a ?

so for now I'll just add your suggested fix, and disclaimer that task names ending in digits won't be supported unless you have two-digit run indices and use the --legacy-tasknames flag.

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madisoth commented 3 years ago

Ahh that makes sense now that you explained it, I'm getting confused by my own code. Merging now.

DCAN-Labs / dcan_bold_processing

regex changes, fixes for abcd-hcp-pipeline + nhp-abcd-bids-pipeline #15