Fmriprep error help

Hi,

Does anyone know how to address these two errors in fmriprep please?

fmriprep_wf.single_subject_013_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol

Node Name: _t1_conform0!

Thanks!

Thank you for reaching out for help - I don’t see any errors on your post.

As per https://fmriprep.readthedocs.io/en/latest/usage.html#troubleshooting, you’ll find some logs under <output dir>/fmriprep/sub-013/log/

Ok sorry about that !

Here’s the error from subject 13:
Node: fmriprep_wf.single_subject_013_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol
Working directory: /data/project/AUT/data/mri_analysis/rs/fmriprep_workdir/fmriprep_wf/single_subject_013_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol

Node inputs:

FLAIR_file =
T1_files =
T2_file =
args =
big_ventricles =
brainstem =
directive = autorecon2-volonly
environ = {}
expert =
flags =
hemi =
hippocampal_subfields_T1 =
hippocampal_subfields_T2 =
hires =
mprage =
mri_aparc2aseg =
mri_ca_label =
mri_ca_normalize =
mri_ca_register =
mri_edit_wm_with_aseg =
mri_em_register =
mri_fill =
mri_mask =
mri_normalize =
mri_pretess =
mri_remove_neck =
mri_segment =
mri_segstats =
mri_tessellate =
mri_watershed =
mris_anatomical_stats =
mris_ca_label =
mris_fix_topology =
mris_inflate =
mris_make_surfaces =
mris_register =
mris_smooth =
mris_sphere =
mris_surf2vol =
mrisp_paint =
openmp = 8
parallel =
subject_id = sub-013
subjects_dir = /data/project/AUT/data/mri_analysis/rs/fmriprep_processed/freesurfer
talairach =
use_FLAIR =
use_T2 =
xopts =

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 479, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 569, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 662, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 382, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 767, in _run_interface
self.raise_exception(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 704, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
recon-all -autorecon2-volonly -openmp 8 -subjid sub-013 -sd /data/project/AUT/data/mri_analysis/rs/fmriprep_processed/freesurfer -nogcareg -nocanorm -nocareg -nonormalization2 -nomaskbfs -nosegmentation -nofill
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
INFO: SUBJECTS_DIR is /data/project/AUT/data/mri_analysis/rs/fmriprep_processed/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rw-rw---- 1 k1517096 aut 180081 Oct 23 03:20 /data/project/AUT/data/mri_analysis/rs/fmriprep_processed/freesurfer/sub-013/scripts/recon-all.log
Linux grid01.nan.kcl.ac.uk 3.10.0-1062.1.2.el7.x86_64 #1 SMP Fri Sep 20 08:24:10 CDT 2019 x86_64 x86_64 x86_64 GNU/Linux

ERROR: it appears that recon-all is already running
for sub-013 based on the presence of /data/project/AUT/data/mri_analysis/rs/fmriprep_processed/freesurfer/sub-013/scripts/IsRunning.rh. It could
also be that recon-all was running at one point but
died in an unexpected way. If it is the case that there
is a process running, you can kill it and start over or
just let it run. If the process has died, you should type:

rm /data/project/AUT/data/mri_analysis/rs/fmriprep_processed/freesurfer/sub-013/scripts/IsRunning.rh

and re-run. Or you can add -no-isrunning to the recon-all
command-line. The contents of this file are:


SUBJECT sub-013
HEMI rh
DATE Fri Oct 18 03:17:23 BST 2019
USER k1517096
HOST grid10.nan.kcl.ac.uk
PROCESSID 30558
PROCESSOR x86_64
OS Linux
Linux grid10.nan.kcl.ac.uk 3.10.0-957.21.3.el7.x86_64 #1 SMP Mon Jun 17 13:37:56 CDT 2019 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $

Standard error:

Return code: 1

And the one from seccond subject:
Node: _t1_conform0
Working directory: /data/project/AUT/data/mri_analysis/rs/fmriprep_workdir/fmriprep_wf/single_subject_019_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0

Node inputs:

in_file = /data/project/AUT/data/mri_analysis/rs/BIDS_data/sub-019/ses-A/anat/sub-019_ses-A_T1w.nii
target_shape = (160, 484, 484)
target_zooms = (1.0, 0.5289255976676941, 0.5289255976676941)

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 479, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 569, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 662, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 382, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/images.py”, line 275, in _run_interface
data = nli.resample_img(reoriented, target_affine, target_shape).get_data()
File “/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py”, line 479, in resample_img
raise BoundingBoxError("The field of view given "
nilearn.image.resampling.BoundingBoxError: The field of view given by the target affine does not contain any of the data

Thanks a lot.

The first error contains a description of the problem and how to solve it:

ERROR: it appears that recon-all is already running
for sub-013 based on the presence of /data/project/AUT/data/mri_analysis/rs/fmriprep_processed/freesurfer/sub-013/scripts/IsRunning.rh. It could
also be that recon-all was running at one point but
died in an unexpected way. If it is the case that there
is a process running, you can kill it and start over or
just let it run. If the process has died, you should type:

rm /data/project/AUT/data/mri_analysis/rs/fmriprep_processed/freesurfer/sub-013/scripts/IsRunning.rh

For the second error, it’s going to be hard to assess without your individual files. Are you able to share them, or defaced versions of them?

Regarding the first error, there’s more info here https://fmriprep.readthedocs.io/en/latest/faq.html#error-it-appears-that-recon-all-is-already-running

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