fMRIPrep issues with multiecho fMRI

Hi @oesteban,

I got the same issue when processing multi-echo data. ( https://github.com/poldracklab/fmriprep/issues/1774 , Question - fmriprep - multi echo data processing).
After going thorough this post and your suggestions, I tried to use FSL( 5.0.6 and 5.0.10 instated of 6.0.0). Those are the only available versions installed on our cluster. I can request them(our cluster IT) to install 5.0.9 or 5.0.11 if you they are much suitable for fMRIprep multi echo pre processing.

Did you get a time to use FSL (6.0.0) for fMRIprep multi-echo prep processing?

Do you know why we are getting these errors when we process multi-echo data? Because so far I processed 3 subjects single echo data without any of these issue.

Now I am getting following issue; Have you seen this before,

fmriprep_wf.single_subject_13023_wf.func_preproc_ses_1_task_Insight2_run_01_echo_1_wf.bold_t2smap_wf.t2smap_node
File: /gpfs/projects/fmriprep/test_s_outputs/fmriprep/sub-13023/log/20190918-105230_0ea46072-7050-4b56-b098-056cba66db1b/crash-20190918-111659-sabeykoon-t2smap_node-e12ae1b9-f4be-4c67-9ee3-3d169f0f01f7.txt
Working Directory: /gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/bold_t2smap_wf/t2smap_node
Inputs: 
args:
echo_times: [0.0108, 0.02868, 0.04656]
environ: {}
in_files: ['/gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-1_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz', '/gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-2_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz', '/gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-3_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz']
Traceback (most recent call last):
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 369, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 752, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 689, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
t2smap -d /gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-1_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz /gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-2_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz /gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-3_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz -e 10.8 28.68 46.559999999999995
Standard output:

Standard error:
/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
INFO:tedana.workflows.t2smap:Loading input data: ['/gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-1_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz', '/gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-2_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz', '/gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/skullstrip_bold_wf/_bold_file_..gpfs..projects..fmriprep..test..sub-13023..ses-1..func..sub-13023_ses-1_task-Insight2_run-01_echo-3_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz']
INFO:tedana.workflows.t2smap:Creating output directory: /gpfs/projects/fmriprep/test_s_outputs/derivatives/scratch/fmriprep_wf/single_subject_13023_wf/func_preproc_ses_1_task_Insight2_run_01_echo_1_wf/bold_t2smap_wf/t2smap_node/TED.vol0000_xform-00000_merged_masked
INFO:tedana.workflows.t2smap:Computing adaptive mask
INFO:tedana.workflows.t2smap:Computing adaptive T2* map
Traceback (most recent call last):
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/bin/t2smap", line 11, in 
    sys.exit(_main())
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/tedana/workflows/t2smap.py", line 226, in _main
    t2smap_workflow(**vars(options))
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/tedana/workflows/t2smap.py", line 185, in t2smap_workflow
    t2s_full, s0_full) = decay.fit_decay(catd, tes, mask, masksum)
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/tedana/decay.py", line 90, in fit_decay
    betas = np.linalg.lstsq(X, log_data, rcond=None)[0]
  File "/gpfs/software/Anaconda3/envs/fmriprep1.2.5/lib/python3.6/site-packages/numpy/linalg/linalg.py", line 1961, in lstsq
    0, work, -1, iwork, 0)
TypeError: must be real number, not NoneType
Return code: 1

Thanks is advance,
Best,
Sameera

Hi @sameera2004,

In order to get the ball rolling, you’ll need to separate the different sources of issues to address them separatelly. In https://github.com/poldracklab/fmriprep/issues/1774 you posted what looks like a synchronization issue. If you believe the issues mentioned here are related, then please follow up there.

Then you ask about FSL versions:

Here you refer to an old MRIQC post which is potentially unrelated. At this point, you haven’t mentioned how you are running fMRIPrep. Please let us know whether you are using a singularity image or a custom installation. Then, please let us know what made you think the version of FSL was causing problems.

Finally, you mention this last error after INFO:tedana.workflows.t2smap:Computing adaptive T2* map. It seems that a problem was found when computing the T2* map. I’ll rope @emdupre in at this point, since she is the most knowledgeable person on that topic.

This is being addressed in https://github.com/poldracklab/fmriprep/issues/1782

1 Like

Thank you! I seems to be running smoothly now.