qsirecon error in 0.19.1: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe2 in position 4095: unexpected end of data #664

cookpa · 2023-12-01T19:22:48Z

I'm possibly doing something wrong here, but I can't figure out why I see this error.

I'm calling qsirecon with this spec

{
  "name": "dsistudio_pipeline",
  "space": "T1w",
  "atlases": ["schaefer100", "schaefer200", "schaefer400", "brainnetome246", "aicha384", "gordon333", "aal116"],
  "nodes": [
    {
      "name": "dsistudio_gqi",
      "software": "DSI Studio",
      "action": "reconstruction",
      "input": "qsiprep",
      "output_suffix": "gqi",
      "parameters": {"method": "gqi"}
    },
    {
      "name": "scalar_export",
      "software": "DSI Studio",
      "action": "export",
      "input": "dsistudio_gqi",
      "output_suffix": "gqiscalar"
    },
    {
      "name": "tractography",
      "software": "DSI Studio",
      "action": "tractography",
      "input": "dsistudio_gqi",
      "parameters": {
        "turning_angle": 35,
        "smoothing": 0.0,
        "step_size": 1.0,
        "min_length": 30,
        "max_length": 250,
        "seed_plan": 0,
        "interpolation": 0,
        "initial_dir": 2,
        "fiber_count": 5000000
      }
    },
    {
      "name": "streamline_connectivity",
      "software": "DSI Studio",
      "action": "connectivity",
      "input": "tractography",
      "output_suffix": "gqinetwork",
      "parameters": {
        "connectivity_value": "count,ncount,mean_length,gfa",
        "connectivity_type": "pass,end"
      }
    }
  ]
}

taken from the repository file under qsiprep/data/pipelines/dsi_studio_gqi.json

The runscript is

module load singularity

image=/project/ftdc_pipeline/ftdc-picsl/pmacsPreps-0.2.3/containers/qsiprep-0.19.1.sif

export SINGULARITYENV_TMPDIR=/tmp

tmpDir=`mktemp -d -p /scratch/pac`

echo "Using tmp dir $tmpDir"

singularity run \
  --containall \
  -B ${tmpDir}:/tmp,/appl/freesurfer-7.1.1/license.txt:/freesurfer/license.txt \
  -B $PWD/output_old:/data/output,/project/ftdc_misc/harmonization/analysis/synb0/bids:/data/bids,${PWD}/dsi_studio_gqi.json:/recon/spec.json \
  $image /data/bids /data/output participant \
  --participant_label HM01 \
  --recon-spec /recon/spec.json \
  --recon_input /data/output \
  --recon-only \
  --nthreads 1 \
  --omp-nthreads 1 \
  --work-dir /tmp \
  --fs-license-file /freesurfer/license.txt

It gets through the tractography stage but fails on connectivity with

231201-12:20:28,664 nipype.workflow INFO:
	 [Node] Finished "gordon333", elapsed time 32.833375s.
231201-12:20:28,664 nipype.workflow WARNING:
	 Storing result file without outputs
231201-12:20:28,666 nipype.workflow WARNING:
	 [Node] Error on "dsistudio_atlasgraph.gordon333" (/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/gordon333)
231201-12:20:28,671 nipype.workflow ERROR:
	 Node gordon333 failed to run on host ftdc-gpu01.
231201-12:20:28,675 nipype.workflow ERROR:
	 Saving crash info to /home/cookpa/crash-20231201-122028-cookpa-gordon333-e4aa145f-b0aa-41af-9094-de25420677f1.pklz
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/linear.py", line 47, in run
    node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node gordon333.

Cmdline:
	dsi_studio --action=ana  --connectivity=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_anat_wf/get_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-Gordon333Ext_desc-LPS_dseg_to_dwi.nii.gz --connectivity_type=pass,end --connectivity_value=count,ncount,mean_length,gfa --source=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/gordon333/sub-HM01_ses-SC3Tx20231019x1312_acq-MultiShellDir117_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.gz --thread_count=1 --thread_count=1 --tract=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/gordon333/sub-HM01_ses-SC3Tx20231019x1312_acq-MultiShellDir117_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.trk.gz
Stdout:

Stderr:

Traceback:
	Traceback (most recent call last):
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run
	    runtime = self._run_interface(runtime)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 764, in _run_interface
	    runtime = run_command(
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/subprocess.py", line 141, in run_command
	    _process()
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/subprocess.py", line 137, in _process
	    stream.read(drain)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/subprocess.py", line 42, in read
	    while self._read(drain) is not None:
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/subprocess.py", line 49, in _read
	    buf = os.read(fd, 4096).decode(self.default_encoding)
	UnicodeDecodeError: 'utf-8' codec can't decode bytes in position 4094-4095: unexpected end of data

I get this same error for all the atlases. I see this error with qsiprep 0.19.1 and 0.18.1, but not 0.16.1

The text was updated successfully, but these errors were encountered:

mattcieslak · 2023-12-01T19:34:15Z

This is a new one, I wonder if it's having trouble reading some of the characters in the DSI Studio output? The newer dsi studios print out fancy status messages.

Can you run your singularity command with singularity shell instead of singularity run and try interactively running the failed command?

cookpa · 2023-12-01T21:10:52Z

Traceback:
	Traceback (most recent call last):
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run
	    runtime = self._run_interface(runtime)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/dsi_studio.py", line 490, in _run_interface
	    wf_result = workflow.run()
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
	    runner.run(execgraph, updatehash=updatehash, config=self.config)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/linear.py", line 82, in run
	    raise error from cause
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/linear.py", line 47, in run
	    node.run(updatehash=updatehash)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
	    result = self._run_interface(execute=True)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
	    return self._run_command(execute)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
	    raise NodeExecutionError(msg)
	nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node schaefer400.

	Cmdline:
		dsi_studio --action=ana  --connectivity=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_anat_wf/get_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-Schaefer2018Ext_desc-400Parcels7NetworksLPS_dseg_to_dwi.nii.gz --connectivity_type=pass,end --connectivity_value=count,ncount,mean_length,gfa --source=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/schaefer400/sub-HM01_ses-SC3Tx20231019x1312_acq-MultiShellDir117_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.gz --thread_count=1 --thread_count=1 --tract=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/schaefer400/sub-HM01_ses-SC3Tx20231019x1312_acq-MultiShellDir117_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.trk.gz

From a shell,

dsi_studio --action=ana  --connectivity=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_anat_wf/get_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-Schaefer2018Ext_desc-400Parcels7NetworksLPS_dseg_to_dwi.nii.gz --connectivity_type=pass,end --connectivity_value=count,ncount,mean_length,gfa --source=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/schaefer400/sub-HM01_ses-SC3Tx20231019x1312_acq-MultiShellDir117_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.gz --thread_count=1 --thread_count=1 --tract=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/schaefer400/sub-HM01_ses-SC3Tx20231019x1312_acq-MultiShellDir117_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.trk.gz

works with just a warning Warning: --thread_count is not used/recognized. Did you mean --end_point ?

cookpa · 2023-12-01T21:24:20Z

I ran qsiprep from within the shell, and I get the error.

qsiprep /data/bids /data/output participant   --participant_label HM01   --recon-spec /recon/spec.json   --recon_input /data/output   --recon-only   --nthreads 1   --omp-nthreads 1   --work-dir /tmp   --fs-license-file /freesurfer/license.txt

But I can run dsi_studio directly

mattcieslak · 2023-12-01T22:13:47Z

ok that's helpful, it's not an issue with dsi studio's print-outs. If the dsi_studio command wrote out any files?

cookpa · 2023-12-01T22:37:46Z

Yes, it is writing a bunch of .mat files

cookpa · 2023-12-06T16:30:14Z

Adding a crash report for context

To summarize:

Using qsiprep 0.19.1
Running qsiprep on the raw data with '--recon-spec dsi_studio_gqi' works, the prep and the recon steps both run successfully
Running qsirecon post-processing with '--recon-only' and the recon spec ' --recon-spec dsi_studio_gqi.json' fails on "Node calc_connectivity"
I can shell into the container and paste the dsi_studio command from the error message, and it runs successfully
Running the same qsiprep post-processing command works with qsiprep 0.16.1, but fails with 0.18.1

Node: qsirecon_wf.sub-HM01_dsistudio_pipeline.sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf.streamline_connectivity.calc_connectivity
Working directory: /tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity

Node inputs:

args = <undefined>
atlas_config = <undefined>
atlas_configs = <undefined>
atlas_name = <undefined>
connectivity = <undefined>
connectivity_type = pass,end
connectivity_value = count,ncount,mean_length,gfa
environ = {}
fa_threshold = <undefined>
fiber_count = <undefined>
initial_dir = <undefined>
input_fib = <undefined>
interpo_angle = <undefined>
interpolation = <undefined>
max_length = <undefined>
min_length = <undefined>
num_threads = 1
random_seed = <undefined>
seed_count = <undefined>
seed_file = <undefined>
seed_plan = <undefined>
smoothing = <undefined>
step_size = <undefined>
thread_count = 1
to_export = <undefined>
trk_file = <undefined>
turning_angle = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node calc_connectivity.

Traceback:
	Traceback (most recent call last):
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run
	    runtime = self._run_interface(runtime)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/dsi_studio.py", line 490, in _run_interface
	    wf_result = workflow.run()
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
	    runner.run(execgraph, updatehash=updatehash, config=self.config)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/linear.py", line 82, in run
	    raise error from cause
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/linear.py", line 47, in run
	    node.run(updatehash=updatehash)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
	    result = self._run_interface(execute=True)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
	    return self._run_command(execute)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
	    raise NodeExecutionError(msg)
	nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node schaefer200.

	Cmdline:
		dsi_studio --action=ana  --connectivity=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_anat_wf/get_atlases/tpl-MNI152NLin2009cAsym_res-01_atlas-Schaefer2018Ext_desc-200Parcels7NetworksLPS_dseg_to_dwi.nii.gz --connectivity_type=pass,end --connectivity_value=count,ncount,mean_length,gfa --source=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/schaefer200/sub-HM01_ses-SC3Tx20231019x1312_acq-MultiShellDir117_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.gz --thread_count=1 --thread_count=1 --tract=/tmp/qsirecon_wf/sub-HM01_dsistudio_pipeline/sub_HM01_ses_SC3Tx20231019x1312_acq_MultiShellDir117_space_T1w_desc_preproc_recon_wf/streamline_connectivity/calc_connectivity/dsistudio_atlasgraph/schaefer200/sub-HM01_ses-SC3Tx20231019x1312_acq-MultiShellDir117_space-T1w_desc-preproc_dwi.src.gz.odf.gqi.1.25.fib.trk.gz
	Stdout:

	Stderr:

	Traceback:
		Traceback (most recent call last):
		  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run
		    runtime = self._run_interface(runtime)
		  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 764, in _run_interface
		    runtime = run_command(
		  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/subprocess.py", line 141, in run_command
		    _process()
		  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/subprocess.py", line 137, in _process
		    stream.read(drain)
		  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/subprocess.py", line 42, in read
		    while self._read(drain) is not None:
		  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/subprocess.py", line 49, in _read
		    buf = os.read(fd, 4096).decode(self.default_encoding)
		UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe2 in position 4095: unexpected end of data

mattcieslak · 2023-12-06T20:29:15Z

Would you be able to share the problematic data with me? We can switch to email to figure out how to transfer

cookpa · 2023-12-06T20:42:15Z

Yes definitely

mattcieslak · 2023-12-11T16:24:49Z

Updating here for posterity: This error only arises in single thread mode.

mattcieslak · 2023-12-11T17:15:14Z

I'm going to update python in the qsiprep image to a higher version, maybe a newer version of python multiprocessing will help with this and some of the hanging issues in the current qsiprep.

mattcieslak · 2024-01-11T17:55:32Z

@cookpa when you get a chance could you see if the current unstable tag works for you? I'm hoping that upgrading to python 3.10 will fix the multiprocessing-related issues (possibly related nipy/nipype#3209)

cookpa · 2024-01-11T21:29:37Z

@mattcieslak Running now. I noticed a backwards compatibility issue. It used to be that I could run with --recon_input /data/output, and it would find data under /data/output/qsiprep/. Now that fails with the error below.

240111-16:18:07,724 nipype.workflow IMPORTANT:
	 
    Running qsirecon version 0.19.2.dev13+g13225c4.d20240110:
      * BIDS dataset path: /data/bids.
      * Participant list: ['HM01'].
      * Run identifier: 20240111-161806_19d42e55-609d-4ce3-9ba2-14d06dc96904.
    
240111-16:18:07,777 nipype.workflow INFO:
	 sub-HM01 not in /data/output, trying recon_input=/data/output/qsiprep
240111-16:18:07,998 nipype.workflow INFO:
	 found ['/data/output/qsiprep/sub-HM01/ses-SC3Tx20231019x1312/dwi/sub-HM01_ses-SC3Tx20231019x1312_acq-MultiShellDir117_space-T1w_desc-preproc_dwi.nii.gz'] in /data/output/qsiprep
240111-16:18:07,999 nipype.workflow INFO:
	 Missing T1w QSIPrep outputs found: /data/output/sub-HM01/anat/sub-HM01_desc-brain_mask.nii.gz /data/output/sub-HM01/anat/sub-HM01_desc-preproc_T1w.nii.gz
240111-16:18:08,0 nipype.workflow INFO:
	 Missing T1w QSIPrep outputs: /data/output/sub-HM01/anat/sub-HM01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 /data/output/sub-HM01/anat/sub-HM01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
Process Process-2:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py", line 1198, in build_recon_workflow
    retval['workflow'] = init_qsirecon_wf(
  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/workflows/recon/base.py", line 99, in init_qsirecon_wf
    single_subject_wf = init_single_subject_wf(
  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/workflows/recon/base.py", line 208, in init_single_subject_wf
    anat_ingress_node, available_anatomical_data = init_highres_recon_anatomical_wf(
  File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/workflows/recon/anatomical.py", line 95, in init_highres_recon_anatomical_wf
    raise Exception("Cannot compute to-template")
Exception: Cannot compute to-template

It's running now that I put --recon_input /data/output/qsiprep. Will report once it finishes

cookpa · 2024-01-11T21:57:47Z

Still failing with a single thread - BTW did I pull the right version?

singularity build qsiprep-unstable.sif docker://pennbbl/qsiprep:unstable

I ask because I still see python 3.8 in the error messages

mattcieslak · 2024-01-11T22:12:33Z

ah! The build failed and never pushed https://app.circleci.com/pipelines/github/PennLINC/qsiprep/1603/workflows/3a356882-3b86-4a17-8016-8cad3c89a26d rerunning it now

mattcieslak · 2024-01-11T23:39:56Z

just checked the most recent unstable and it's now python 3.10.13, sorry for the confusion

cookpa · 2024-01-12T00:32:16Z

@mattcieslak got it, but I'm still seeing the same Unicode error, unfortunately

cookpa · 2024-01-12T01:20:47Z

Still works with 2 threads

mattcieslak · 2024-01-12T02:13:25Z

oh that's disappointing. Is using 2 threads ok for now? I might have to bump this to the next milestone

cookpa · 2024-01-12T02:35:55Z

Sounds good, I'm fine with using two threads for now.

closes #664

mattcieslak added this to the 0.20 milestone Dec 11, 2023

mattcieslak self-assigned this Dec 11, 2023

This was referenced Jan 10, 2024

[ENH] Update python version to 3.10 PennLINC/qsiprep_build#7

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[ENH] Update to python 3.10 #670

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mattcieslak modified the milestones: 0.20, 0.21 Jan 12, 2024

mattcieslak added a commit that referenced this issue Mar 5, 2024

closes #664

a17222b

mattcieslak mentioned this issue Mar 5, 2024

[FIX] Prevent undecodable terminal output in calc_connectivity #711

Merged

mattcieslak added a commit that referenced this issue Mar 5, 2024

[FIX] Prevent undecodable terminal output in calc_connectivity (#711)

51ca838

closes #664

mattcieslak closed this as completed in #711 Mar 5, 2024

mattcieslak added a commit that referenced this issue Mar 5, 2024

[FIX] Prevent undecodable terminal output in calc_connectivity (#711)

ca99272

closes #664

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qsirecon error in 0.19.1: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe2 in position 4095: unexpected end of data #664

qsirecon error in 0.19.1: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe2 in position 4095: unexpected end of data #664

cookpa commented Dec 1, 2023

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cookpa commented Dec 6, 2023

mattcieslak commented Dec 11, 2023

mattcieslak commented Dec 11, 2023

mattcieslak commented Jan 11, 2024

cookpa commented Jan 11, 2024

cookpa commented Jan 11, 2024

mattcieslak commented Jan 11, 2024

mattcieslak commented Jan 11, 2024

cookpa commented Jan 12, 2024

cookpa commented Jan 12, 2024

mattcieslak commented Jan 12, 2024

cookpa commented Jan 12, 2024

qsirecon error in 0.19.1: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe2 in position 4095: unexpected end of data #664

qsirecon error in 0.19.1: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe2 in position 4095: unexpected end of data #664

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