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