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How can I convert an unprocessed folder only have T1 and DWI? #11

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zhangjb35 opened this issue Jun 22, 2021 · 0 comments
Open

How can I convert an unprocessed folder only have T1 and DWI? #11

zhangjb35 opened this issue Jun 22, 2021 · 0 comments

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@zhangjb35
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zhangjb35 commented Jun 22, 2021

Here is my tree of folder:
└── unprocessed
└── 3T
├── 100206_3T.csv
├── Diffusion
│   ├── 100206_3T_BIAS_32CH.nii.gz
│   ├── 100206_3T_BIAS_BC.nii.gz
│   ├── 100206_3T_DWI_dir95_LR.bval
│   ├── 100206_3T_DWI_dir95_LR.bvec
│   ├── 100206_3T_DWI_dir95_LR.nii.gz
│   ├── 100206_3T_DWI_dir95_LR_SBRef.nii.gz
│   ├── 100206_3T_DWI_dir95_RL.bval
│   ├── 100206_3T_DWI_dir95_RL.bvec
│   ├── 100206_3T_DWI_dir95_RL.nii.gz
│   ├── 100206_3T_DWI_dir95_RL_SBRef.nii.gz
│   ├── 100206_3T_DWI_dir96_LR.bval
│   ├── 100206_3T_DWI_dir96_LR.bvec
│   ├── 100206_3T_DWI_dir96_LR.nii.gz
│   ├── 100206_3T_DWI_dir96_LR_SBRef.nii.gz
│   ├── 100206_3T_DWI_dir96_RL.bval
│   ├── 100206_3T_DWI_dir96_RL.bvec
│   ├── 100206_3T_DWI_dir96_RL.nii.gz
│   ├── 100206_3T_DWI_dir96_RL_SBRef.nii.gz
│   ├── 100206_3T_DWI_dir97_LR.bval
│   ├── 100206_3T_DWI_dir97_LR.bvec
│   ├── 100206_3T_DWI_dir97_LR.nii.gz
│   ├── 100206_3T_DWI_dir97_LR_SBRef.nii.gz
│   ├── 100206_3T_DWI_dir97_RL.bval
│   ├── 100206_3T_DWI_dir97_RL.bvec
│   ├── 100206_3T_DWI_dir97_RL.nii.gz
│   ├── 100206_3T_DWI_dir97_RL_SBRef.nii.gz
│   └── LINKED_DATA
│   └── PHYSIO
│   ├── 100206_3T_DWI_dir95_LR_Physio_log.txt
│   ├── 100206_3T_DWI_dir95_RL_Physio_log.txt
│   ├── 100206_3T_DWI_dir96_LR_Physio_log.txt
│   ├── 100206_3T_DWI_dir96_RL_Physio_log.txt
│   ├── 100206_3T_DWI_dir97_LR_Physio_log.txt
│   └── 100206_3T_DWI_dir97_RL_Physio_log.txt
├── T1w_MPR1
│   ├── 100206_3T_AFI.nii.gz
│   ├── 100206_3T_BIAS_32CH.nii.gz
│   ├── 100206_3T_BIAS_BC.nii.gz
│   ├── 100206_3T_FieldMap_Magnitude.nii.gz
│   ├── 100206_3T_FieldMap_Phase.nii.gz
│   └── 100206_3T_T1w_MPR1.nii.gz
└── T2w_SPC1
├── 100206_3T_AFI.nii.gz
├── 100206_3T_BIAS_32CH.nii.gz
├── 100206_3T_BIAS_BC.nii.gz
├── 100206_3T_FieldMap_Magnitude.nii.gz
├── 100206_3T_FieldMap_Phase.nii.gz
└── 100206_3T_T2w_SPC1.nii.gz

When I run hcp2bids, they throw this error:
intended_for - anat/sub-100206_run-01_T1w.nii.gz

BIDS format data is at - /Users/jinb/Documents/datapool/dataset_example/HCP-1200-DWI/BIDS/100206/

Running arrange_subjects

Running json_toplevel
its RL
Traceback (most recent call last):
File "hcp2bids-master/hcp2bids/main.py", line 693, in
main()
File "hcp2bids-master/hcp2bids/main.py", line 690, in main
json_toplevel(output_dir)
File "hcp2bids-master/hcp2bids/main.py", line 589, in json_toplevel
task=json_file.split('_')[0].split('-')[1]
IndexError: list index out of range

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