how to get fs_LR space bold data from hcppipeline

[Yuan Cao]

Hi expert,

I have recently been running XCP-D using hcp-preprocessed data, but an error indicated that I lacked fs_LR spaced bold data. I am wondering which step in hcppipeline can create fs_LR space data. Is the task-rest_dir-RL_LR_Atlas_MSMAll.dtseries.nii the 32k_fsLR space data? Attached is my Results folder

Here is the code I used and the error:

Code:

sudo docker run -it --rm -v /media/ubuntu/NCU/deng/Rawdata:/data -v /media/ubuntu/NCU/out:/out -v /opt/freesurfer/license.txt:/opt/freesurfer/license.txt pennlinc/xcp_d:latest /data /out --despike --head_radius 40 -w /media/ubuntu/NCU/deng/Rawdata --smoothing 6 --fs-license-file /opt/freesurfer/license.txt participant --participant-label 233 --input-type hcp
Error:
With input_type hcp, cifti processing (--cifti) will be enabled automatically.
With input_type hcp, surface normalization (--warp-surfaces-native2std) will be enabled automatically.
240626-00:24:59,480 nipype.utils WARNING:
 convert_hcp2bids is an experimental function.
240626-00:24:59,480 nipype.utils INFO:
 Converting 233
240626-00:24:59,481 nipype.utils WARNING:
 File DNE: /data/233/MNINonLinear/T1w.nii.gz
240626-00:24:59,481 nipype.utils WARNING:
 File DNE: /data/233/MNINonLinear/brainmask_fs.nii.gz
240626-00:24:59,481 nipype.utils WARNING:
 File DNE: /data/233/MNINonLinear/ribbon.nii.gz
240626-00:24:59,481 nipype.utils WARNING:
 File DNE: /data/233/MNINonLinear/aparc+aseg.nii.gz
240626-00:24:59,481 nipype.utils WARNING:
 File DNE: /data/233/MNINonLinear/fsaverage_LR32k/233.L.pial.32k_fs_LR.surf.gii
240626-00:24:59,481 nipype.utils WARNING:
 File DNE: /data/233/MNINonLinear/fsaverage_LR32k/233.R.pial.32k_fs_LR.surf.gii
240626-00:24:59,481 nipype.utils WARNING:
 File DNE: /data/233/MNINonLinear/fsaverage_LR32k/233.L.white.32k_fs_LR.surf.gii
240626-00:24:59,482 nipype.utils WARNING:
 File DNE: /data/233/MNINonLinear/fsaverage_LR32k/233.R.white.32k_fs_LR.surf.gii
240626-00:24:59,482 nipype.utils WARNING:
 File(s) DNE:
/data/233/MNINonLinear/fsaverage_LR32k/233.L.thickness.32k_fs_LR.shape.gii
/data/233/MNINonLinear/fsaverage_LR32k/233.R.thickness.32k_fs_LR.shape.gii
240626-00:24:59,482 nipype.utils WARNING:
 File(s) DNE:
/data/233/MNINonLinear/fsaverage_LR32k/233.L.corrThickness.32k_fs_LR.shape.gii
/data/233/MNINonLinear/fsaverage_LR32k/233.R.corrThickness.32k_fs_LR.shape.gii
240626-00:24:59,482 nipype.utils WARNING:
 File(s) DNE:
/data/233/MNINonLinear/fsaverage_LR32k/233.L.curvature.32k_fs_LR.shape.gii
/data/233/MNINonLinear/fsaverage_LR32k/233.R.curvature.32k_fs_LR.shape.gii
240626-00:24:59,482 nipype.utils WARNING:
 File(s) DNE:
/data/233/MNINonLinear/fsaverage_LR32k/233.L.sulc.32k_fs_LR.shape.gii
/data/233/MNINonLinear/fsaverage_LR32k/233.R.sulc.32k_fs_LR.shape.gii
240626-00:24:59,482 nipype.utils WARNING:
 File(s) DNE:
/data/233/MNINonLinear/fsaverage_LR32k/233.L.MyelinMap.32k_fs_LR.func.gii
/data/233/MNINonLinear/fsaverage_LR32k/233.R.MyelinMap.32k_fs_LR.func.gii
240626-00:24:59,482 nipype.utils WARNING:
 File(s) DNE:
/data/233/MNINonLinear/fsaverage_LR32k/233.L.SmoothedMyelinMap.32k_fs_LR.func.gii
/data/233/MNINonLinear/fsaverage_LR32k/233.R.SmoothedMyelinMap.32k_fs_LR.func.gii
240626-00:24:59,482 nipype.utils INFO:
 Finished collecting anatomical files
240626-00:24:59,482 nipype.utils INFO:
 Finished collecting functional files
240626-00:24:59,482 nipype.utils INFO:
 Copying files
240626-00:24:59,482 nipype.utils WARNING:
 File used for more than one output: /usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/transform/itkIdentityTransform.txt
240626-00:24:59,483 nipype.utils INFO:
 Finished copying files
240626-00:24:59,485 nipype.utils INFO:
 Conversion completed
240626-00:25:07,978 nipype.workflow IMPORTANT:
 Running XCP-D version 0.7.4
240626-00:25:07,984 nipype.workflow IMPORTANT:
 Building XCP-D's workflow:
           * Preprocessing derivatives path: /media/ubuntu/NCU/deng/Rawdata/dset_bids/derivatives/hcp.
           * Participant list: ['233'].
           * Run identifier: 20240626-002456_0bfbfefb-f810-410b-946d-4cbf81cbcc10.
Process Process-2:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/cli/workflow.py", line 98, in build_workflow
    retval["workflow"] = init_xcpd_wf()
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/workflows/base.py", line 80, in init_xcpd_wf
    single_subject_wf = init_single_subject_wf(subject_id)
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/workflows/base.py", line 126, in init_single_subject_wf
    subj_data = collect_data(
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/utils/bids.py", line 255, in collect_data
    raise FileNotFoundError(
FileNotFoundError: No BOLD data found in allowed spaces (fsLR).

Query: {'datatype': 'func', 'suffix': 'bold', 'desc': ['preproc', None], 'extension': '.dtseries.nii', 'space': 'fsLR'}

Thank you so much

Yuan

[Tim Coalson]

The folder screenshot you sent shows preprocessed outputs in a "sub-223" folder, but your command is trying to find files in a "223" folder.  You probably need to specify "sub-223" as the subject identifier.  That output folder looks like someone has tried to use BIDS-like names for the HCP preprocessing outputs, with an unclear amount of success.

Yes, the _Atlas*.dtseries.nii files should contain fs_LR32k data.

Tim

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[Jim Pollaro]

I've run into this problem. It's one of many you'll get trying to get this data to work. xcp-d is good enough to know that 223 is sub-223

Starting on this line of xcp-d you can see the BIDS format it's xcp-d is looking for. My issue was all the bold data was `task<tasktype><run-id>` instead of `task-<task-type>_run-<run-id>`. Once I changed those, it started to work. And now it's failing on trying to collect the brain registration data. I'm getting
```

2024-11-18 15:33:06,030 [ WARNING] WARNING: Cannot detect name collisions for function 'nifti_masker_extractor'

Traceback (most recent call last):

  File "/usr/local/miniconda/bin/xcp_d", line 8, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/cli/run.py", line 27, in main
    parse_args(args=sys.argv[1:])
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/cli/parser.py", line 799, in parse_args
    convert_to_bids(
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/ingression/abcdbids.py", line 73, in convert_dcan2bids
    convert_dcan_to_bids_single_subject(
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/ingression/abcdbids.py", line 298, in convert_dcan_to_bids_single_subject
    collect_hcp_confounds(
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/ingression/utils.py", line 182, in collect_hcp_confounds
    brainreg = pd.DataFrame(
  File "/usr/local/miniconda/lib/python3.10/site-packages/pandas/core/frame.py", line 778, in __init__
    mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
  File "/usr/local/miniconda/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 503, in dict_to_mgr
    return arrays_to_mgr(arrays, columns, index, dtype=dtype, typ=typ, consolidate=copy)
  File "/usr/local/miniconda/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 114, in arrays_to_mgr
    index = _extract_index(arrays)
  File "/usr/local/miniconda/lib/python3.10/site-packages/pandas/core/internals/construction.py", line 677, in _extract_index
    raise ValueError("All arrays must be of the same length")

ValueError: All arrays must be of the same length

```

For some reason the masks or data are different lengths. It's immensely frustrating

[Glasser, Matthew]

What is xcp-d?

Matt.

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