Final BOLD images count is off

[cfilippi4]

What happened?

When trying to run nibabies, I got the error:

filippica@cn0922:/data/filippica/R21/code $ nibabies /data/filippica/R21/BIDS/OIT/ /data/filippica/R21/derivatives/OIT/nibabies participant --participant-label sub-OIT022 -w /data/filippica/R21/tmp/derivatives/OIT/nibabies --age-months 4 --nprocs 1 --omp-nthreads 1 --random-seed 0 --error-on-aroma-warnings -v --fd-spike-threshold .2 --fs-license-file /data/filippica/R21/lists/license.txt
WARNING: While bind mounting '/gs10:/gs10': destination is already in the mount point list
211008-18:17:07,915 cli INFO:
	 Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator@1.5.7

	1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

	Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.


        Summary:                  Available Tasks:        Available Modalities: 
        727 Files, 20.17GB                                T1w                   
        54 - Subjects                                     T2w                   
        52 - Sessions                                     bold                  
                                                          fieldmap              


	If you have any questions, please post on https://neurostars.org/tags/bids.

211008-18:17:24,393 nipype.workflow IMPORTANT:
	 
    Running nibabies version 0.1.2:
      * BIDS dataset path: /data/filippica/R21/BIDS/OIT.
      * Participant list: ['OIT022'].
      * Run identifier: 20211008-181657_b979f989-bfa5-4115-b481-9dcb3ea6a949.
      * Output spaces: None.
      * Pre-run FreeSurfer's SUBJECTS_DIR: /data/filippica/R21/derivatives/OIT/nibabies/freesurfer-infant.
Process Process-2:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/src/nibabies/nibabies/cli/workflow.py", line 82, in build_workflow
    retval["workflow"] = init_nibabies_wf()
  File "/src/nibabies/nibabies/workflows/base.py", line 68, in init_nibabies_wf
    single_subject_wf = init_single_subject_wf(subject_id)
  File "/src/nibabies/nibabies/workflows/base.py", line 417, in init_single_subject_wf
    subject=subject_id
  File "/src/nibabies/nibabies/utils/bids.py", line 187, in group_bolds_ref
    assert len(bolds) == sum([len(x) for x in files]), "Final BOLD images count is off"
AssertionError: Final BOLD images count is off

The functional fMRI data are complete.

I'm not sure what this error means and/or how to resolve. I'm running nibabies version 0.1.2.

I also checked to see if this was a part of the bids validator but got the same error when I added the --skip__bids_validation.

Thanks for your help!

-C

What command did you use?

nibabies /data/filippica/R21/BIDS/OIT/ /data/filippica/R21/derivatives/OIT/nibabies participant --participant-label sub-OIT022 -w /data/filippica/R21/tmp/derivatives/OIT/nibabies --age-months 4 --nprocs 1 --omp-nthreads 1 --random-seed 0 --error-on-aroma-warnings -v --fd-spike-threshold .2 --fs-license-file /data/filippica/R21/lists/license.txt

Version

0.1.2 or older

Relevant log output

No response

Add any additional information or context about the problem here.

No response

[mgxd]

Looks like something is not going when grouping across BOLD runs. Can you run tree /data/filippica/R21/BIDS/OIT/sub-OIT022 and post the output?

I agree that the error message is not very helpful, I will improve it.

[cfilippi4]

[filippica@biowulf BIDS]$ tree /data/filippica/R21/BIDS/OIT/sub-OIT022/
/data/filippica/R21/BIDS/OIT/sub-OIT022/
└── ses-20180607
    ├── anat
    │   ├── sub-OIT022_ses-20180607_run-184837_T1w.json
    │   ├── sub-OIT022_ses-20180607_run-184837_T1w.nii.gz
    │   ├── sub-OIT022_ses-20180607_run-185410_T2w.json
    │   └── sub-OIT022_ses-20180607_run-185410_T2w.nii.gz
    ├── fmap
    │   ├── sub-OIT022_ses-20180607_dir-AP_run-191004_epi.json
    │   ├── sub-OIT022_ses-20180607_dir-AP_run-191004_epi.nii.gz
    │   ├── sub-OIT022_ses-20180607_dir-PA_run-191038_epi.json
    │   └── sub-OIT022_ses-20180607_dir-PA_run-191038_epi.nii.gz
    └── func
        ├── sub-OIT022_ses-20180607_task-rest_run-191152_bold.json
        ├── sub-OIT022_ses-20180607_task-rest_run-191152_bold.nii.gz
        ├── sub-OIT022_ses-20180607_task-rest_run-192225_bold.json
        └── sub-OIT022_ses-20180607_task-rest_run-192225_bold.nii.gz

4 directories, 12 files

[mgxd]

hm, nothing is jumping out at me - I just submitted a patch that should help debug this problem better. Can you try using the latest developmental version and report back with the error message?

It looks like you are running the bare-metal installation, so to use the bleeding edge, you can do:

python -m pip install --upgrade https://github.com/nipreps/nibabies/archive/refs/heads/master.zip

[mgxd]

@cfilippi4 were you able to run it?

Alternatively, if you are able to share a portion of that subject's data with me I should be able to see what's happening. I would essentially just need:

• The metadata (.json) files for the BOLD images
• The image dimensions (you can easily get this if you have nibabel installed by running

$ nib-ls /data/filippica/R21/BIDS/OIT/sub-OIT022/ses-20180607/func/*.gz

[cfilippi4]

Thanks! I was able to run that line...
python -m pip install --upgrade https://github.com/nipreps/nibabies/archive/refs/heads/master.zip

Then the error suggested that we didn't have infant freesurfer so we installed it.

When we re-ran the original line we got the following error, indicating that it doesn't recognize the infant freesurfer version.

[R21] (base) filippica@cn2879:~/2021/OIT-R21/code $ nibabies /data/filippica/R21/BIDS/OIT/ /data/filippica/R21/derivatives/OIT/nibabies participant --participant-label sub-OIT022 -w /data/filippica/R21/tmp/derivatives/OIT/nibabies --age-months 4 --nprocs 1 --omp-nthreads 1 --random-seed 0 --error-on-aroma-warnings -v --fd-spike-threshold .2 --fs-license-file /data/filippica/R21/lists/license.txt --notrack
/data/filippica/R21/code/conda/lib/python3.8/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
  warnings.warn("The ability to pass arguments to BIDSLayout that control "
211013-13:21:59,13 cli INFO:
                Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator does not appear to be installed
Process Process-2:
Traceback (most recent call last):
  File "/data/filippica/R21/code/conda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/filippica/R21/code/conda/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nibabies/cli/workflow.py", line 20, in build_workflow
    from ..workflows.base import init_nibabies_wf
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nibabies/workflows/base.py", line 22, in <module>
    from ..interfaces.reports import SubjectSummary, AboutSummary
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nibabies/interfaces/reports.py", line 22, in <module>
    from smriprep.interfaces.freesurfer import ReconAll
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/smriprep/interfaces/freesurfer.py", line 28, in <module>
    from nipype.interfaces import freesurfer as fs
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nipype/interfaces/freesurfer/__init__.py", line 7, in <module>
    from .preprocess import (
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nipype/interfaces/freesurfer/preprocess.py", line 37, in <module>
    FSVersion = Info.looseversion().vstring
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nipype/interfaces/freesurfer/base.py", line 83, in looseversion
    raise RuntimeError("Unknown version string: " + ver)
RuntimeError: Unknown version string: freesurfer-linux-centos7_x86_64-infant-dev-4a14499-20210109-4a14499

This is the content of one of the .json files...

[filippica@biowulf func]$ cat sub-OIT022_ses-20180607_task-rest_run-191152_bold.json 
{
	"Modality": "MR",
	"MagneticFieldStrength": 3,
	"ImagingFrequency": 123.189,
	"Manufacturer": "Siemens",
	"ManufacturersModelName": "TrioTim",
	"PatientName": "OIT22",
	"PatientID": "OIT22",
	"PatientBirthDate": "2018-02-15",
	"PatientSex": "M",
	"PatientWeight": 5.98742,
	"PatientPosition": "HFS",
	"SoftwareVersions": "syngo MR B17",
	"MRAcquisitionType": "2D",
	"SeriesDescription": "cmrr_F6_R2.0C_TR1250_V480",
	"ProtocolName": "cmrr_F6_R2.0C_TR1250_V480",
	"ScanningSequence": "EP",
	"SequenceVariant": "SK\\SS",
	"ScanOptions": "FS",
	"SequenceName": "epfid2d1_96",
	"ImageType": ["ORIGINAL", "PRIMARY", "M", "MB", "ND", "MOSAIC"],
	"SeriesNumber": 13,
	"AcquisitionTime": "19:11:52.520000",
	"AcquisitionDateTime": "2018-06-07T19:11:52.520000",
	"AcquisitionNumber": 1,
	"ImageComments": "Unaliased MB6/PE3 (remote)",
	"SliceThickness": 2,
	"SpacingBetweenSlices": 2,
	"SAR": 0.182937,
	"EchoTime": 0.0394,
	"RepetitionTime": 1.25,
	"FlipAngle": 90,
	"PartialFourier": 1,
	"BaseResolution": 96,
	"ShimSetting": [
		5196,
		-5357,
		12837,
		784,
		-22,
		1176,
		-6,
		-18	],
	"TxRefAmp": 320.284,
	"PhaseResolution": 1,
	"ReceiveCoilName": "32Ch_Head",
	"CoilString": "C:HEA;HEP",
	"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold",
	"MultibandAccelerationFactor": 6,
	"PercentPhaseFOV": 100,
	"PercentSampling": 100,
	"PhaseEncodingSteps": 96,
	"AcquisitionMatrixPE": 96,
	"ReconMatrixPE": 96,
	"BandwidthPerPixelPhaseEncode": 14.881,
	"EffectiveEchoSpacing": 0.000699998,
	"DerivedVendorReportedEchoSpacing": 0.000699998,
	"TotalReadoutTime": 0.0664998,
	"PixelBandwidth": 1796,
	"DwellTime": 2.9e-06,
	"PhaseEncodingDirection": "j-",
	"SliceTiming": [
		0,
		0.8775,
		0.5025,
		0.125,
		1.005,
		0.6275,
		0.25,
		1.13,
		0.7525,
		0.3775,
		0,
		0.8775,
		0.5025,
		0.125,
		1.005,
		0.6275,
		0.25,
		1.13,
		0.7525,
		0.3775,
		0,
		0.8775,
		0.5025,
		0.125,
		1.005,
		0.6275,
		0.25,
		1.13,
		0.7525,
		0.3775,
		0,
		0.8775,
		0.5025,
		0.125,
		1.005,
		0.6275,
		0.25,
		1.13,
		0.7525,
		0.3775,
		0,
		0.8775,
		0.5025,
		0.125,
		1.005,
		0.6275,
		0.25,
		1.13,
		0.7525,
		0.3775,
		0,
		0.8775,
		0.5025,
		0.125,
		1.005,
		0.6275,
		0.25,
		1.13,
		0.7525,
		0.3775	],
	"ImageOrientationPatientDICOM": [
		0.999949,
		-0.00240274,
		-0.00978657,
		-4.77518e-08,
		0.971158,
		-0.238438	],
	"InPlanePhaseEncodingDirectionDICOM": "COL",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20210317"
}

We also tried to check the image dimensions with the nibabel command you sent but nib-ls is not available.

[cfilippi4]

Oh wait...I tried running nib-ls again with the specific file name instead of the *.gz and I got output.....

filippica@biowulf:/data/filippica/R21/BIDS/OIT/sub-OIT022/ses-20180607/func $ nib-ls sub-OIT022_ses-20180607_task-rest_run-191152_bold.nii.gz 
sub-OIT022_ses-20180607_task-rest_run-191152_bold.nii.gz int16 [ 96,  96,  60, 480] 2.00x2.00x2.00x1.25   sform

filippica@biowulf:/data/filippica/R21/BIDS/OIT/sub-OIT022/ses-20180607/func $ nib-ls sub-OIT022_ses-20180607_task-rest_run-192225_bold.nii.gz 
sub-OIT022_ses-20180607_task-rest_run-192225_bold.nii.gz int16 [ 96,  96,  60, 480] 2.00x2.00x2.00x1.25   sform

[mgxd]

for the FreeSurfer error, you'll have to delete ${FREESURFER_HOME}/build-stamp.txt

Thanks for the information, but can you post sub-OIT022_ses-20180607_task-rest_run-192225_bold.json as well? I'll need it to replicate your issue

[cfilippi4]

Thanks! Below is the second .json file info.

filippica@biowulf:/data/filippica/R21/BIDS/OIT/sub-OIT022/ses-20180607/func $ cat sub-OIT022_ses-20180607_task-rest_run-192225_bold.json 
{
	"Modality": "MR",
	"MagneticFieldStrength": 3,
	"ImagingFrequency": 123.189,
	"Manufacturer": "Siemens",
	"ManufacturersModelName": "TrioTim",
	"PatientName": "OIT22",
	"PatientID": "OIT22",
	"PatientBirthDate": "2018-02-15",
	"PatientSex": "M",
	"PatientWeight": 5.98742,
	"PatientPosition": "HFS",
	"SoftwareVersions": "syngo MR B17",
	"MRAcquisitionType": "2D",
	"SeriesDescription": "cmrr_F6_R2.0C_TR1250_V480_2",
	"ProtocolName": "cmrr_F6_R2.0C_TR1250_V480_2",
	"ScanningSequence": "EP",
	"SequenceVariant": "SK\\SS",
	"ScanOptions": "FS",
	"SequenceName": "epfid2d1_96",
	"ImageType": ["ORIGINAL", "PRIMARY", "M", "MB", "ND", "MOSAIC"],
	"SeriesNumber": 14,
	"AcquisitionTime": "19:22:25.517500",
	"AcquisitionDateTime": "2018-06-07T19:22:25.517500",
	"AcquisitionNumber": 1,
	"ImageComments": "Unaliased MB6/PE3 (remote)",
	"SliceThickness": 2,
	"SpacingBetweenSlices": 2,
	"SAR": 0.183811,
	"EchoTime": 0.0394,
	"RepetitionTime": 1.25,
	"FlipAngle": 90,
	"PartialFourier": 1,
	"BaseResolution": 96,
	"ShimSetting": [
		5196,
		-5357,
		12837,
		784,
		-22,
		1176,
		-6,
		-18	],
	"TxRefAmp": 320.284,
	"PhaseResolution": 1,
	"ReceiveCoilName": "32Ch_Head",
	"CoilString": "C:HEA;HEP",
	"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_bold",
	"MultibandAccelerationFactor": 6,
	"PercentPhaseFOV": 100,
	"PercentSampling": 100,
	"PhaseEncodingSteps": 96,
	"AcquisitionMatrixPE": 96,
	"ReconMatrixPE": 96,
	"BandwidthPerPixelPhaseEncode": 14.881,
	"EffectiveEchoSpacing": 0.000699998,
	"DerivedVendorReportedEchoSpacing": 0.000699998,
	"TotalReadoutTime": 0.0664998,
	"PixelBandwidth": 1796,
	"DwellTime": 2.9e-06,
	"PhaseEncodingDirection": "j-",
	"SliceTiming": [
		0,
		0.88,
		0.5025,
		0.1275,
		1.005,
		0.6275,
		0.2525,
		1.13,
		0.7525,
		0.3775,
		0,
		0.88,
		0.5025,
		0.1275,
		1.005,
		0.6275,
		0.2525,
		1.13,
		0.7525,
		0.3775,
		0,
		0.88,
		0.5025,
		0.1275,
		1.005,
		0.6275,
		0.2525,
		1.13,
		0.7525,
		0.3775,
		0,
		0.88,
		0.5025,
		0.1275,
		1.005,
		0.6275,
		0.2525,
		1.13,
		0.7525,
		0.3775,
		0,
		0.88,
		0.5025,
		0.1275,
		1.005,
		0.6275,
		0.2525,
		1.13,
		0.7525,
		0.3775,
		0,
		0.88,
		0.5025,
		0.1275,
		1.005,
		0.6275,
		0.2525,
		1.13,
		0.7525,
		0.3775	],
	"ImageOrientationPatientDICOM": [
		0.999949,
		-0.00240274,
		-0.00978657,
		-4.77518e-08,
		0.971158,
		-0.238438	],
	"InPlanePhaseEncodingDirectionDICOM": "COL",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20210317"
}

Just a note--to further anonymize the data, I did remove a handful of fields from both. The fields removed are--

"InstitutionName": "",
	"InstitutionalDepartmentName": "",
	"InstitutionAddress": "",
	"DeviceSerialNumber": "",
	"StationName": "",
	"SeriesInstanceUID": "",
	"StudyInstanceUID": "",
	"ReferringPhysicianName": "",
	"StudyID": "",
	"ProcedureStepDescription": "",

[mgxd]

Thanks. I was not able to replicate this using the latest development version. Are you still running into this after updating nibabies?

[cfilippi4]

Yes, I ran...
python -m pip install --upgrade https://github.com/nipreps/nibabies/archive/refs/heads/master.zip

The version now listed is....
filippica@cn0943:/data/filippica/R21 $ nibabies --version
NiBabies v0+unknown

I removed the build-stamp.txt (as suggested above). Now I get another error--similar to the original but more specifically about grouping BOLD runs.

Command run:
nibabies /data/filippica/R21/BIDS/OIT/ /data/filippica/R21/derivatives/OIT/nibabies participant --participant-label sub-OIT022 -w /data/filippica/R21/tmp/derivatives/OIT/nibabies --age-months 4 --nprocs 1 --omp-nthreads 1 --random-seed 0 --error-on-aroma-warnings -v --fd-spike-threshold .2 --fs-license-file /data/filippica/R21/lists/license.txt --notrack

Error:

filippica@cn0943:/data/filippica/R21 $ nibabies /data/filippica/R21/BIDS/OIT/ /data/filippica/R21/derivatives/OIT/nibabies participant --participant-label sub-OIT022 -w /data/filippica/R21/tmp/derivatives/OIT/nibabies --age-months 4 --nprocs 1 --omp-nthreads 1 --random-seed 0 --error-on-aroma-warnings -v --fd-spike-threshold .2 --fs-license-file /data/filippica/R21/lists/license.txt --notrack

/data/filippica/R21/code/conda/lib/python3.8/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
  warnings.warn("The ability to pass arguments to BIDSLayout that control "
211013-15:56:56,794 cli INFO:
	 Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator does not appear to be installed
/data/filippica/R21/code/conda/lib/python3.8/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
  warnings.warn("The ability to pass arguments to BIDSLayout that control "
211013-15:57:19,499 nipype.workflow IMPORTANT:
	 
    Running nibabies version 0+unknown:
      * BIDS dataset path: /data/filippica/R21/BIDS/OIT.
      * Participant list: ['OIT022'].
      * Run identifier: 20211013-155646_a2c71c63-8c4d-4f69-8dfb-a02aa546475a.
      * Output spaces: None.
      * Pre-run FreeSurfer's SUBJECTS_DIR: /data/filippica/R21/derivatives/OIT/nibabies/sourcedata/infant-freesurfer.
/data/filippica/R21/code/conda/lib/python3.8/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
  warn("Fetchers from the nilearn.datasets module will be "
211013-15:57:40,981 nipype.interface WARNING:
	 FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
Process Process-2:
Traceback (most recent call last):
  File "/data/filippica/R21/code/conda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/filippica/R21/code/conda/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nibabies/cli/workflow.py", line 80, in build_workflow
    retval["workflow"] = init_nibabies_wf()
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nibabies/workflows/base.py", line 68, in init_nibabies_wf
    single_subject_wf = init_single_subject_wf(subject_id)
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nibabies/workflows/base.py", line 404, in init_single_subject_wf
    _, bold_groupings = group_bolds_ref(layout=config.execution.layout, subject=subject_id)
  File "/data/filippica/R21/code/conda/lib/python3.8/site-packages/nibabies/utils/bids.py", line 204, in group_bolds_ref
    raise RuntimeError(msg)
RuntimeError: Error encountered when grouping BOLD runs.
Combinations: [('20180607', 'j-', 0.0664998)]
Sorted files: [['/data/filippica/R21/BIDS/OIT/sub-OIT022/ses-20180607/func/sub-OIT022_ses-20180607_task-rest_run-191152_bold.nii.gz', '/data/filippica/R21/BIDS/OIT/sub-OIT022/ses-20180607/func/sub-OIT022_ses-20180607_task-rest_run-192225_bold.nii.gz']]
BOLD files: []

Please share this information with the nibabies developers at:
https://github.com/nipreps/nibabies/issues/new/choose

[mgxd]

Thanks for the quick reply - I think this might be happening because you are using an older version of pybids.

Can you also run

python -m pip install --upgrade pybids

and then retry?

[cfilippi4]

Same problem....See below...

[R21] (base) filippica@cn0943:/data/filippica/R21 $ python -m pip install --upgrade pybids
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: pybids in ./code/conda/lib/python3.8/site-packages (0.13.2)
Requirement already satisfied: click in ./code/conda/lib/python3.8/site-packages (from pybids) (8.0.1)
Requirement already satisfied: num2words in ./code/conda/lib/python3.8/site-packages (from pybids) (0.5.10)
Requirement already satisfied: numpy in ./code/conda/lib/python3.8/site-packages (from pybids) (1.20.3)
Requirement already satisfied: nibabel>=2.1 in ./code/conda/lib/python3.8/site-packages (from pybids) (3.2.1)
Requirement already satisfied: sqlalchemy<1.4.0.dev0 in ./code/conda/lib/python3.8/site-packages (from pybids) (1.3.24)
Requirement already satisfied: pandas>=0.23 in ./code/conda/lib/python3.8/site-packages (from pybids) (1.3.2)
Requirement already satisfied: patsy in ./code/conda/lib/python3.8/site-packages (from pybids) (0.5.1)
Requirement already satisfied: bids-validator in ./code/conda/lib/python3.8/site-packages (from pybids) (1.8.4)
Requirement already satisfied: scipy in ./code/conda/lib/python3.8/site-packages (from pybids) (1.6.2)
Requirement already satisfied: packaging>=14.3 in ./code/conda/lib/python3.8/site-packages (from nibabel>=2.1->pybids) (21.0)
Requirement already satisfied: pyparsing>=2.0.2 in ./code/conda/lib/python3.8/site-packages (from packaging>=14.3->nibabel>=2.1->pybids) (2.4.7)
Requirement already satisfied: python-dateutil>=2.7.3 in ./code/conda/lib/python3.8/site-packages (from pandas>=0.23->pybids) (2.8.2)
Requirement already satisfied: pytz>=2017.3 in ./code/conda/lib/python3.8/site-packages (from pandas>=0.23->pybids) (2021.1)
Requirement already satisfied: six>=1.5 in ./code/conda/lib/python3.8/site-packages (from python-dateutil>=2.7.3->pandas>=0.23->pybids) (1.16.0)
Requirement already satisfied: docopt>=0.6.2 in ./code/conda/lib/python3.8/site-packages (from num2words->pybids) (0.6.2)
[R21] (base) filippica@cn0943:/data/filippica/R21 $ nibabies /data/filippica/R21/BIDS/OIT/ /data/filippica/R21/derivatives/OIT/nibabies participant --participant-label sub-OIT022 -w /data/filippica/R21/tmp/derivatives/OIT/nibabies --age-months 4 --nprocs 1 --omp-nthreads 1 --random-seed 0 --error-on-aroma-warnings -v --fd-spike-threshold .2 --fs-license-file /data/filippica/R21/lists/license.txt --notrack
/data/filippica/R21/code/conda/lib/python3.8/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
  warnings.warn("The ability to pass arguments to BIDSLayout that control "
211013-16:31:12,437 cli INFO:
	 Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator does not appear to be installed
/data/filippica/R21/code/conda/lib/python3.8/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
  warnings.warn("The ability to pass arguments to BIDSLayout that control "
211013-16:31:38,260 nipype.workflow IMPORTANT:
	 
    Running nibabies version 0+unknown:
      * BIDS dataset path: /data/filippica/R21/BIDS/OIT.
      * Participant list: ['OIT022'].
      * Run identifier: 20211013-163101_870d6e99-94c8-4ae6-829a-0a1e77f9bfe7.
      * Output spaces: MNIInfant:cohort-2:res-native.
      * Pre-run FreeSurfer's SUBJECTS_DIR: /data/filippica/R21/derivatives/OIT/nibabies/sourcedata/infant-freesurfer.
/data/filippica/R21/code/conda/lib/python3.8/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
  warn("Fetchers from the nilearn.datasets module will be "
211013-16:32:00,843 nipype.interface WARNING:
	 FSLOUTPUTTYPE environment variable is not set. Setting FSLOUTPUTTYPE=NIFTI
Process Process-2:
Traceback (most recent call last):
  File "/data/filippica/R21/code/conda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/data/filippica/R21/code/conda/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/home/filippica/.local/lib/python3.8/site-packages/nibabies/cli/workflow.py", line 80, in build_workflow
    retval["workflow"] = init_nibabies_wf()
  File "/home/filippica/.local/lib/python3.8/site-packages/nibabies/workflows/base.py", line 68, in init_nibabies_wf
    single_subject_wf = init_single_subject_wf(subject_id)
  File "/home/filippica/.local/lib/python3.8/site-packages/nibabies/workflows/base.py", line 404, in init_single_subject_wf
    _, bold_groupings = group_bolds_ref(layout=config.execution.layout, subject=subject_id)
  File "/home/filippica/.local/lib/python3.8/site-packages/nibabies/utils/bids.py", line 204, in group_bolds_ref
    raise RuntimeError(msg)
RuntimeError: Error encountered when grouping BOLD runs.
Combinations: [('20180607', 'j-', 0.0664998)]
Sorted files: [['/data/filippica/R21/BIDS/OIT/sub-OIT022/ses-20180607/func/sub-OIT022_ses-20180607_task-rest_run-191152_bold.nii.gz', '/data/filippica/R21/BIDS/OIT/sub-OIT022/ses-20180607/func/sub-OIT022_ses-20180607_task-rest_run-192225_bold.nii.gz']]
BOLD files: []