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rmarkello / pypmi

A very small toolbox for working with data from the Parkinson's Progression Markers Initiative (PPMI)
https://pypmi.readthedocs.io
BSD 3-Clause "New" or "Revised" License
14 stars 8 forks source link

Cannot correctly turn PPMI dataset by pypmi (herdiconv) #19

Open jojowang-17 opened 8 months ago

jojowang-17 commented 8 months ago

Hi,

I tried to use the pypmi to turn the PPMI to BIDS. I tested on 3 subjects using the following code

import pypmi.bids pypmi.bids.convert_ppmi(raw_dir='data/raw/ppmi/dicoms', out_dir='data/raw/ppmi/bids', ignore_bad=True coerce_study_uids=True)

But it cannot work correctly. The output of the code is INFO: Generated sequence info for 17 studies with 10752 entries total WARNING: Skipping unrecognized series description: 3 PLANE LOC WARNING: Skipping unrecognized series description: MIDLINE SAG LOC WARNING: Skipping unrecognized series description: SAG 3D MPRAGE WARNING: Skipping unrecognized series description: 3D T2 FLAIR_ND WARNING: Skipping unrecognized series description: 3D T2 FLAIR WARNING: Skipping unrecognized series description: RESTING STATE FMRI ep2d_fid_basic_bold WARNING: Skipping unrecognized series description: RESTING STATE FMRI ep2d_fid_basic_bold

I have tested the lastest version of heudiconv docker image. Still the same warning information!

Thanks!

nateRaw3 commented 6 months ago

has this issue been resolved, i cannot get the convert_ppmi function to process any recent participants downloaded from PPMI. Similar errors with unrecognized series description. I am interested in seeing if this is just an independent issue or if something changed.