Second pass error

[hbaagil]

Hi, I am new to resting state fMRI. First of all, thank you for this, it certainly is a useful tool. I am working with an online dataset PPMI from multiple sites. I have 2 questions: 1.) in the PPMI manual it says: Please note: Two Axial Resting State fMRI (BOLD) sequences must be acquired. The initial sequence (Phase encoding direction R>L), and a repeat sequence (Phase encoding direction L>R) to correct for distortion. Does this means the second sequence should be in the fmap BIDS directory? 2.) The first pass conversion works fine, however for the second pass I am facing some issues (please see below).

Processing subject 100898

Working subject directory : /Users/hamzah/Desktop/PPMI_rsfMRI_GI/00_rsfMRI_RL/work/sub-100898 BIDS subject directory : /Users/hamzah/Desktop/PPMI_rsfMRI_GI/00_rsfMRI_RL/sub-100898 Organizing SAG_3D_T1_FSPGR Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.10/bin/bidskit", line 8, in sys.exit(main()) File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/bidskit/main.py", line 289, in main d2n.organize_series( File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/bidskit/dcm2niix.py", line 166, in organize_series prot_dict = fmaps.add_intended_run(prot_dict, src_meta, run_no[fc]) File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/bidskit/fmaps.py", line 413, in add_intended_run if prot_dict[info['SerDesc']] in suffixes: KeyError: 'SerDesc'

Thank you very much in advance! Hamzah

[hbaagil]

The Protocol_Translator.json looks something like this: { "3D_T1__weighted":[ "anat", "T1w", "UNASSIGNED" ], "rsfMRI_L_R":[ "fmap",
"acq-rest", ["task-rest_bold"]
], "rsfMRI_RL":[ "func",
"task-rest_bold",
"UNASSIGNED" ] }

Am I doing something wrong?

Cheers, Hamzah

[jmtyszka]

Hi @hbaagil Looks like are a couple of things going on with the protocol translator setup, but first things first, which version of bidskit and dcm2niix are you using? Let me know - later versions may fix your SerDesc error.

[jmtyszka]

For the RL and LR encoded rs-fMRI runs, I'd put both of them in the func folder and add dir-RL and dir-LR to the BIDS file stubs in the Protocol_Translator.json, so something like this:

{
    "3D_T1__weighted":[
        "anat",
        "T1w",
        "UNASSIGNED"
    ],
    "rsfMRI_L_R":[
        "func",
        "task-rest_dir-LR_bold",
        "UNASSIGNED"
    ],
    "rsfMRI_RL":[
        "func",
        "task-rest_dir-RL_bold",
        "UNASSIGNED"
    ],
}

Quick note: you won't get great results using T2*-weighted EPI with phase encoding reversal (RL and LR) for susceptibility distortion correction (SDC). Does the PPMI project acquire SE-EPI, DW-EPI or multiecho GRE fieldmap data as part of its protocol?. If so you could estimate distortion corrections for the T2*-EPI from the DW-EPI data if its acquired with phase encoding reversal. If PPMI has a recommended preprocessing pipeline, definitely use that.

[hbaagil]

Hi @jmtyszka, thank you for your quick response. I am using: BIDSKIT 2022.8.26 dcm2niiX version v1.0.20220720

The PPMI database also acquire DW-EPI. Unfortunately, there is no recommended preprocessing pipeline from PPMI.

Cheers!

[hbaagil]

@jmtyszka I did as you suggested, but now I get this error message from the [email protected]

(node:1642) Warning: Closing directory handle on garbage collection (Use node --trace-warnings ... to show where the warning was created) 1: [ERR] You have to define 'TaskName' for this file. (code: 50 - TASK_NAME_MUST_DEFINE) ./sub-100878/func/sub-100878_task-rest_dir-LR_bold.nii.gz ./sub-100878/func/sub-100878_task-rest_dir-RL_bold.nii.gz ./sub-101124/func/sub-101124_task-rest_dir-LR_bold.nii.gz ./sub-101124/func/sub-101124_task-rest_dir-RL_bold.nii.gz ./sub-101175/func/sub-101175_task-rest_dir-LR_bold.nii.gz ./sub-101175/func/sub-101175_task-rest_dir-RL_bold.nii.gz ./sub-101179/func/sub-101179_task-rest_dir-LR_bold.nii.gz ./sub-101179/func/sub-101179_task-rest_dir-RL_bold.nii.gz ./sub-101492/func/sub-101492_task-rest_dir-LR_bold.nii.gz ./sub-101492/func/sub-101492_task-rest_dir-RL_bold.nii.gz ... and 40 more files having this issue (Use --verbose to see them all).

I am assuming that the 2 files with distinct LR and RL phase encoding is causing this error in the func directory?

[jmtyszka]

Try upgrading bidskit to v2022.10.4, clearing your work and sub-* folders and re-running bidskit. Looks like the TaskName field in the JSON sidecars hasn't been filled. Let me know how if the bids-validator still complains after the re-conversion.