Summary of what happened:
Hi,
I am running fmriprep and getting the following error. I would really appreciate any help! Please let me know if more information should be provided!
Thanks so much,
tengwen
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep-docker /Users/Desktop/WL_fMRI/data/BIDS /Users/Desktop/WL_fMRI/data/derivatives/fmriprep participant --participant-label sub-WLfMRI035 --fs-license-file /Users/Desktop/WL_fMRI/license.txt --bids-filter-file /Users/Desktop/WL_fMRI/anat_filter_JMS.py
Version:
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Stderr:
makeIsotropic WARNING: not different enough, won't reslice!
Killed
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._post_run_hook(runtime)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/freesurfer.py", line 248, in _post_run_hook
fix_lta_length(lta_file)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/freesurfer.py", line 399, in fix_lta_length
lines = Path(lta_file).read_text().splitlines(keepends=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/pathlib.py", line 1134, in read_text
with self.open(mode='r', encoding=encoding, errors=errors) as f:
File "/opt/conda/envs/fmriprep/lib/python3.10/pathlib.py", line 1119, in open
return self._accessor.open(self, mode, buffering, encoding, errors,
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/work/fmriprep_23_2_wf/sub_WLfMRI033_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta'
Screenshots / relevant information:
It seems that this happened during the Registration:
Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
Type Source : 0 Type Target : 3 ensure both FLOAT (3)
Reordering axes in mov to better fit dst... ( -1 -3 2 )
Determinant after swap : 1
Mov: (0.5, 0.5, 0.5)mm and dim (512, 512, 512)
Dst: (0.5, 0.5, 0.5)mm and dim (360, 512, 512)
Asserting both images: 0.5mm isotropic
- reslicing Mov ...
-- changing data type from 0 to 3 (noscale = 0)...
- reslicing Dst ...
-- Original : (0.5, 0.5, 0.5)mm and (360, 512, 512) voxels.
-- Resampled: (0.5, 0.5, 0.5)mm and (512, 512, 512) voxels.
-- Reslicing using cubic bspline
MRItoBSpline degree 3
- WARNING: trg mri outside_val = 0 but suspected background: -0.00687514
If background is black or darkgray, ignore this. If white, pass --whitebgdst
Registration::findSaturation
- computing centroids
- computing initial transform
-- using translation info
- Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
- Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 )
- Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 )
- Max Resolution used: 3
-- gpS ( 64 , 64 , 64 )
-- gpT ( 64 , 64 , 64 )
- running loop to estimate saturation parameter:
-- Iteration: 1 trying sat: 16
min sat: 0 ( -1 ), max sat: 16 ( 0.12101 ), sat diff: 16, (wlimit=0.16)
-- Iteration: 2 trying sat: 8
min sat: 8 ( 0.324589 ), max sat: 16 ( 0.12101 ), sat diff: 8, (wlimit=0.16)
-- Iteration: 3 trying sat: 12
min sat: 12 ( 0.193726 ), max sat: 16 ( 0.12101 ), sat diff: 4, (wlimit=0.16)
-- Iteration: 4 trying sat: 14
min sat: 12 ( 0.193726 ), max sat: 14 ( 0.15173 ), sat diff: 2, (wlimit=0.16)
-- Iteration: 5 trying sat: 13
min sat: 13 ( 0.17074 ), max sat: 14 ( 0.15173 ), sat diff: 1, (wlimit=0.16)
-- Iteration: 6 trying sat: 13.5
- final SAT: 14 ( it: 6 , weight check 0.15173 <= 0.16 )
Registration::computeMultiresRegistration
- computing centroids
- computing initial transform
-- using translation info
- Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
- initial transform:
Ti = [ ...
1.0000000000000 0 0 1.6982521922295
0 1.0000000000000 0 -1.1595074345649
0 0 1.0000000000000 -1.1415599519338
0 0 0 1.0000000000000 ]
- initial iscale: Ii =1