Fmriprep v1.4.0 error when using fsLR in output-spaces

1

Hi,

This is the first time I am using --output-spaces, so I maybe my fmriprep command is wrong. When using “fsLR” in --output-spaces, fmriprep exits with errors. Here is my fmriprep command:

~/anaconda3/bin/fmriprep-docker \
    /data/jheffernan/clinical/bids /data/jheffernan/clinical/derivatives/fmriprep-local participant \
    --participant_label 14461002 \
    -t rest \
    --ignore slicetiming \
    --output-spaces MNI152NLin2009cAsym fsaverage fsLR \
    --dummy-scans 2 \
    --fs-license-file /opt/freesurfer/license.txt \
    --work-dir /data/jheffernan/clinical/work_dir2 \
    --notrack

Here are the errors displayed in the terminal:

[Node] Running "save_midthickness" ("nipype.interfaces.io.DataSink")
190610-15:44:57,713 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_14461002_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness".
190610-15:45:47,978 nipype.workflow INFO:
	 [Node] Setting-up "_sampler1" in "/scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1".
190610-15:45:47,982 nipype.workflow INFO:
	 [Node] Running "_sampler1" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi rh --interp trilinear --o /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1/rh.fsLR.gii  --srcsubject sub-14461002 --reg /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii --trgsubject fsLR
190610-15:45:51,395 nipype.workflow WARNING:
	 [Node] Error on "_sampler1" (/scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1)
190610-15:45:51,501 nipype.workflow ERROR:
	 Node _sampler1 failed to run on host 6268c8fd74df.
190610-15:45:51,503 nipype.workflow ERROR:
	 Saving crash info to /out/fmriprep/sub-14461002/log/20190610-154018_ba368a98-49e7-42ca-9f98-ec0080f2b56d/crash-20190610-154551-root-_sampler1-d4abcfee-e6e6-4c19-a36d-788d156359bc.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
    return super(FSCommand, self).run(**inputs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
mri_vol2surf --cortex --hemi rh --interp trilinear --o /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1/rh.fsLR.gii  --srcsubject sub-14461002 --reg /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii --trgsubject fsLR
Standard output:
srcvol = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii
srcreg = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/set_xfm_source/out_concat.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsLR
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
INFO: overriding regsubject  with sub-14461002
Input reg is LTA
-------- original matrix -----------
-1.00000  -0.00023  -0.00008  -0.99401;
-0.00008  -0.00007   1.00000  -17.94840;
 0.00023  -1.00000  -0.00007  -9.98506;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /out/freesurfer/fsLR/label/rh.cortex.label
Standard error:
No such file or directory
mri_vol2surf: could not open label file /out/freesurfer/fsLR/label/rh.cortex.label
Invalid argument
mri_vol2surf: could not load label file /out/freesurfer/fsLR/label/rh.cortex.label
Invalid argument
Return code: 255

190610-15:45:53,675 nipype.workflow INFO:
	 [Node] Setting-up "_sampler1" in "/scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler1".
190610-15:45:53,678 nipype.workflow INFO:
	 [Node] Running "_sampler1" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi lh --interp trilinear --o /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler1/lh.fsLR.gii  --srcsubject sub-14461002 --reg /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii --trgsubject fsLR
190610-15:45:55,264 nipype.workflow WARNING:
	 [Node] Error on "_sampler1" (/scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler1)
190610-15:45:55,504 nipype.workflow ERROR:
	 Node _sampler1 failed to run on host 6268c8fd74df.
190610-15:45:55,505 nipype.workflow ERROR:
	 Saving crash info to /out/fmriprep/sub-14461002/log/20190610-154018_ba368a98-49e7-42ca-9f98-ec0080f2b56d/crash-20190610-154555-root-_sampler1-0deb04ce-7b0e-434f-88b8-fbf6662da092.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
    return super(FSCommand, self).run(**inputs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
mri_vol2surf --cortex --hemi lh --interp trilinear --o /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler1/lh.fsLR.gii  --srcsubject sub-14461002 --reg /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii --trgsubject fsLR
Standard output:
srcvol = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii
srcreg = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/set_xfm_source/out_concat.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsLR
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
INFO: overriding regsubject  with sub-14461002
Input reg is LTA
-------- original matrix -----------
-1.00000  -0.00023  -0.00008  -0.99401;
-0.00008  -0.00007   1.00000  -17.94840;
 0.00023  -1.00000  -0.00007  -9.98506;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /out/freesurfer/fsLR/label/lh.cortex.label
Standard error:
No such file or directory
mri_vol2surf: could not open label file /out/freesurfer/fsLR/label/lh.cortex.label
Invalid argument
mri_vol2surf: could not load label file /out/freesurfer/fsLR/label/lh.cortex.label
Invalid argument
Return code: 255

190610-15:46:03,958 nipype.workflow INFO:
	 [Node] Setting-up "_sampler1" in "/scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1".
190610-15:46:03,961 nipype.workflow INFO:
	 [Node] Running "_sampler1" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi rh --interp trilinear --o /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1/rh.fsLR.gii  --srcsubject sub-14461002 --reg /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii --trgsubject fsLR
190610-15:46:03,962 nipype.workflow INFO:
	 [Node] Setting-up "_sampler1" in "/scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler1".
190610-15:46:03,967 nipype.workflow INFO:
	 [Node] Running "_sampler1" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi lh --interp trilinear --o /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler1/lh.fsLR.gii  --srcsubject sub-14461002 --reg /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii --trgsubject fsLR
190610-15:46:07,290 nipype.workflow WARNING:
	 [Node] Error on "_sampler1" (/scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1)
190610-15:46:07,322 nipype.workflow WARNING:
	 [Node] Error on "_sampler1" (/scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler1)
190610-15:46:07,838 nipype.workflow ERROR:
	 Node _sampler1 failed to run on host 6268c8fd74df.
190610-15:46:07,838 nipype.workflow ERROR:
	 Saving crash info to /out/fmriprep/sub-14461002/log/20190610-154018_ba368a98-49e7-42ca-9f98-ec0080f2b56d/crash-20190610-154607-root-_sampler1-6db9ddbc-7167-4b7e-ab69-b1daeaf9dc5a.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
    return super(FSCommand, self).run(**inputs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
mri_vol2surf --cortex --hemi rh --interp trilinear --o /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1/rh.fsLR.gii  --srcsubject sub-14461002 --reg /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii --trgsubject fsLR
Standard output:
srcvol = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii
srcreg = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/set_xfm_source/out_concat.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsLR
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
INFO: overriding regsubject  with sub-14461002
Input reg is LTA
-------- original matrix -----------
-1.00000  -0.00023  -0.00008  -0.99401;
-0.00008  -0.00007   1.00000  -17.94840;
 0.00023  -1.00000  -0.00007  -9.98506;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /out/freesurfer/fsLR/label/rh.cortex.label
Standard error:
No such file or directory
mri_vol2surf: could not open label file /out/freesurfer/fsLR/label/rh.cortex.label
Invalid argument
mri_vol2surf: could not load label file /out/freesurfer/fsLR/label/rh.cortex.label
Invalid argument
Return code: 255

190610-15:46:07,841 nipype.workflow ERROR:
	 Node _sampler1 failed to run on host 6268c8fd74df.
190610-15:46:07,841 nipype.workflow ERROR:
	 Saving crash info to /out/fmriprep/sub-14461002/log/20190610-154018_ba368a98-49e7-42ca-9f98-ec0080f2b56d/crash-20190610-154607-root-_sampler1-1ab4d5a8-a0e3-4437-92e3-1d3847bb61c6.txt
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
    return super(FSCommand, self).run(**inputs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
mri_vol2surf --cortex --hemi lh --interp trilinear --o /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler1/lh.fsLR.gii  --srcsubject sub-14461002 --reg /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii --trgsubject fsLR
Standard output:
srcvol = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii
srcreg = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_1_wf/bold_surf_wf/set_xfm_source/out_concat.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsLR
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
INFO: overriding regsubject  with sub-14461002
Input reg is LTA
-------- original matrix -----------
-1.00000  -0.00023  -0.00008  -0.99401;
-0.00008  -0.00007   1.00000  -17.94840;
 0.00023  -1.00000  -0.00007  -9.98506;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /out/freesurfer/fsLR/label/lh.cortex.label
Standard error:
No such file or directory
mri_vol2surf: could not open label file /out/freesurfer/fsLR/label/lh.cortex.label
Invalid argument
mri_vol2surf: could not load label file /out/freesurfer/fsLR/label/lh.cortex.label
Invalid argument
Return code: 255

190610-15:50:08,506 nipype.workflow ERROR:
	 could not run node: fmriprep_wf.single_subject_14461002_wf.func_preproc_task_rest_dir_RL_run_2_wf.bold_surf_wf.sampler.aI.a1
190610-15:50:08,507 nipype.workflow ERROR:
	 could not run node: fmriprep_wf.single_subject_14461002_wf.func_preproc_task_rest_dir_RL_run_2_wf.bold_surf_wf.sampler.aI.a0
190610-15:50:08,507 nipype.workflow ERROR:
	 could not run node: fmriprep_wf.single_subject_14461002_wf.func_preproc_task_rest_dir_RL_run_1_wf.bold_surf_wf.sampler.aI.a1
190610-15:50:08,507 nipype.workflow ERROR:
	 could not run node: fmriprep_wf.single_subject_14461002_wf.func_preproc_task_rest_dir_RL_run_1_wf.bold_surf_wf.sampler.aI.a0
fMRIPrep failed: Workflow did not execute cleanly. Check log for details
Preprocessing did not finish successfully. Errors occurred while processing data from participants: 14461002 (4). Check the HTML reports for details.
fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues

Here are the contents of the crash info text file (crash-20190610-154551-root-_sampler1-d4abcfee-e6e6-4c19-a36d-788d156359bc.txt):

Node: _sampler1
Working directory: /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1

Node inputs:

apply_rot = <undefined>
apply_trans = <undefined>
args = <undefined>
cortex_mask = True
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'}
fix_tk_reg = <undefined>
float2int_method = <undefined>
frame = <undefined>
hemi = rh
hits_file = <undefined>
hits_type = <undefined>
ico_order = <undefined>
interp_method = trilinear
mask_label = <undefined>
mni152reg = <undefined>
no_reshape = <undefined>
out_file = <undefined>
out_type = gii
override_reg_subj = True
projection_stem = <undefined>
reference_file = <undefined>
reg_file = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/set_xfm_source/out_concat.lta
reg_header = <undefined>
reshape = <undefined>
reshape_slices = <undefined>
sampling_method = average
sampling_range = (0.0, 1.0, 0.2)
sampling_units = frac
scale_input = <undefined>
smooth_surf = <undefined>
smooth_vol = <undefined>
source_file = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii
subject_id = sub-14461002
subjects_dir = /out/freesurfer
surf_reg = <undefined>
surface = <undefined>
target_subject = fsLR
vox_file = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
    return super(FSCommand, self).run(**inputs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
mri_vol2surf --cortex --hemi rh --interp trilinear --o /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler1/rh.fsLR.gii  --srcsubject sub-14461002 --reg /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii --trgsubject fsLR
Standard output:
srcvol = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/rename_src/mapflow/_rename_src1/fsLR.nii
srcreg = /scratch/fmriprep_wf/single_subject_14461002_wf/func_preproc_task_rest_dir_RL_run_2_wf/bold_surf_wf/set_xfm_source/out_concat.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsLR
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
INFO: overriding regsubject  with sub-14461002
Input reg is LTA
-------- original matrix -----------
-1.00000  -0.00023  -0.00008  -0.99401;
-0.00008  -0.00007   1.00000  -17.94840;
 0.00023  -1.00000  -0.00007  -9.98506;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /out/freesurfer/fsLR/label/rh.cortex.label
Standard error:
No such file or directory
mri_vol2surf: could not open label file /out/freesurfer/fsLR/label/rh.cortex.label
Invalid argument
mri_vol2surf: could not load label file /out/freesurfer/fsLR/label/rh.cortex.label
Invalid argument
Return code: 255
2

Hi, by the looks of the crashfile this seems like a problem during FreeSurfer. Please check first whether the file truly exists (/data/jheffernan/clinical/derivatives/fmriprep-local/freesurfer/fsLR/label/rh.cortex.label)

Second, please revise the memory settings of your docker engine. It is very possible that the file was not created because of a memory problem.

3

The file /data/jheffernan/clinical/derivatives/fmriprep-local/freesurfer/fsLR/label/rh.cortex.label does not exist. There is no fsLR directory within the freesurfer directory.

In terms of memory, I receive this warning message from nipype when running fmriprep on one data set:

190611-17:04:07,726 nipype.workflow WARNING:
	 Some nodes exceed the total amount of memory available (28.21GB).
4

I’ve been revising this issue and came to realize that there are several issues we need to fix before fsLR can be used as one output space - please follow up here https://github.com/poldracklab/fmriprep/issues/1673

5

A post was split to a new topic: Error running FreeSurfer via fMRIPrep

6

Hello,

I have run into a similar issue when trying to use fsLR as an output space. I am running fmriprep using singularity (HPC system).

I have set my memory to 40G and am not getting any warnings regarding memory.
I have also made sure that my working directory is clean, as per this thread: Error running FreeSurfer via fMRIPrep

Here is the command I ran:
export SINGULARITYENV_TEMPLATEFLOW_HOME="${myproject}/templateflow" # Tell fMRIPrep the mount point

singularity run -B “${myproject}”:"${myproject}" --cleanenv “${myproject}/fmriprep-1.5.8.simg” “${myproject}/PNC_bids_full” “${myproject}/output_fsLR” participant --participant-label “${SUBJECT}” --fs-license-file “${myproject}/license.txt” --use-aroma --use-syn-sdc --cifti-output --medial-surface-nan --output-spaces fsLR -w /tmp/ --skip_bids_validation

Being a new user, I cannot upload my output file. However, from what I can see, this is the relevant error:
Loading label /data/cephfs/punim0675/fmriprep/fmriprep_full_PNC/output_fsLR/freesurfer/fsLR/label/rh.cortex.label
Standard error:
No such file or directory
mri_vol2surf: could not open label file /data/cephfs/punim0675/fmriprep/fmriprep_full_PNC/output_fsLR/freesurfer/fsLR/label/rh.cortex.label
Invalid argument
mri_vol2surf: could not load label file /data/cephfs/punim0675/fmriprep/fmriprep_full_PNC/output_fsLR/freesurfer/fsLR/label/rh.cortex.label
Invalid argument
Return code: 255

In the FreeSurfer directory, there is no fsLR directory, only fsaverage, fsaverage5 and sub.

Do you have any suggestions on how to troubleshoot this?

Thanks

7

This error was resolved after using v 20.0.0
Thank you for the update.