External Email - Use Caution
Hi Freesurfer folks,
I'm running Freesurfer's longitudinal pipeline as part of FMRIprep and I've
got two subjects generating similar errors in the mri_robust_template step,
one of which I've copied below. I've defaced these subjects and saved the
working directories so I can share them with you on the ftp site if you'd
like.
Thanks for your help,
Dylan Nielson
Error for subject 22477:
RuntimeError: Command:
mri_robust_template --satit --mov
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz
--inittp 1 --iscale --template
sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_template.nii.gz
--subsample 200 --lta
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta
Standard output:
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
--satit: Will estimate SAT iteratively!
--mov: Using
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
as movable/source volume.
--mov: Using
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
as movable/source volume.
--mov: Using
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
as movable/source volume.
--mov: Using
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz
as movable/source volume.
Total: 4 input volumes
--inittp: Using TP 1 as target for initialization
--iscale: Enableing intensity scaling!
--template: Using
sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_template.nii.gz as
template output volume.
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
Setting iscale ...
reading source
'/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'...
converting source
'/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'
to bspline ...
MRItoBSpline degree 3
reading source
'/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'...
converting source
'/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'
to bspline ...
MRItoBSpline degree 3
reading source
'/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'...
converting source
'/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz'
to bspline ...
MRItoBSpline degree 3
reading source
'/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz'...
converting source
'/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz'
to bspline ...
MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5
, epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ==============================
Register TP 2 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
)
to TP 1 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
)
[init] ========================= TP 4 to TP 1 ==============================
Register TP 4 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz
)
to TP 1 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
)
[init] ========================= TP 3 to TP 1 ==============================
Register TP 3 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
)
to TP 1 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
)
- Max Resolution used: 2
-- gpS ( 51 , 64 , 64 )
-- gpT ( 51 , 64 , 64 )
- running loop to estimate saturation parameter:
- Max Resolution used: 2
-- gpS ( 51 , 64 , 64 )
-- gpT ( 51 , 64 , 64 )
- running loop to estimate saturation parameter:
- Max Resolution used: 2
-- gpS ( 51 , 64 , 64 )
-- gpT ( 51 , 64 , 64 )
- running loop to estimate saturation parameter:
* WARNING: TP 2 to 1 did not converge !!
* WARNING: TP 3 to 1 did not converge !!
* WARNING: TP 4 to 1 did not converge !!
Input rotation's max deviation from rotation is: 6.17523e-05
computing mean coord of TP 1 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-22477_ses-01_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
)
mapping back to rot, err = 1.92296e-16
computing mean coord of TP 2 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-22477_ses-02_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
)
mapping back to rot, err = 5.2975e-15
computing mean coord of TP 3 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-22477_ses-03_acq-mprage_rec-ORIG_run-1_T1w_ras_corrected.nii.gz
)
mapping back to rot, err = 7.55033e-16
computing mean coord of TP 4 (
/lscratch/33515238/wrk/fmriprep_wf/single_subject_22477_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-22477_ses-04_acq-mprageABCD_rec-ORIG_run-1_T1w_corrected.nii.gz
)
Standard error:Internal Error for tp 3 -> template
Rotation should not scale ( 3.08776e-05 )
Debug Info:
A = [ ...
0.9969922338242 -0.0778269037878 0.0033377292333
0.0777901549173 0.9969203604879 0.0099370478686
-0.0041009199390 -0.0096472102695 0.9999450558122 ]
R = [ ...
0.9969614041457 -0.0778255626866 0.0033377292333
0.0777890868352 0.9969203142925 0.0099370478686
-0.0041008064181 -0.0096472142869 0.9999450558122 ]
S = [ ...
1.0000308195503 -0.0000013334491 -0.0000000000000
-0.0000013334491 1.0000001503863 0.0000000000000
-0.0000000000000 0.0000000000000 1.0000000000000 ]
Internal Error: Rotation should not scale.
Return code: 248
Error for subject 24028:
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 265, in run
return super(FSCommandOpenMP, self).run(**inputs)
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_robust_template --satit --mov
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz
--inittp 1 --iscale --template
sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_template.nii.gz
--subsample 200 --lta
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta
Standard output:
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
--satit: Will estimate SAT iteratively!
--mov: Using
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz
as movable/source volume.
--mov: Using
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz
as movable/source volume.
Total: 2 input volumes
--inittp: Using TP 1 as target for initialization
--iscale: Enableing intensity scaling!
--template: Using
sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_template.nii.gz as
template output volume.
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
Setting iscale ...
reading source
'/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz'...
converting source
'/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz'
to bspline ...
MRItoBSpline degree 3
reading source
'/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz'...
converting source
'/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz'
to bspline ...
MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5
, epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ==============================
Register TP 2 (
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz
)
to TP 1 (
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz
)
- Max Resolution used: 2
-- gpS ( 43 , 64 , 64 )
-- gpT ( 43 , 64 , 64 )
- running loop to estimate saturation parameter:
* WARNING: TP 2 to 1 did not converge !!
Input rotation's max deviation from rotation is: 4.27526e-05
computing mean coord of TP 1 (
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-24028_ses-01_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz
)
mapping back to rot, err = 0
computing mean coord of TP 2 (
/lscratch/33514484/wrk/fmriprep_wf/single_subject_24028_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-24028_ses-02_acq-mprage_rec-ORIG_run-1_T1w_corrected.nii.gz
)
Standard error:Internal Error for tp 1 -> template
Rotation should not scale ( 2.13756e-05 )
Debug Info:
A = [ ...
0.9976866765353 0.0613358758176 0.0285823594087
-0.0624208989520 0.9972963115456 0.0387788304011
-0.0261239538328 -0.0404768298397 0.9988387368875 ]
R = [ ...
0.9977078546957 0.0613362673314 0.0285814448261
-0.0624218986995 0.9972961437200 0.0387802563678
-0.0261255285353 -0.0404754744389 0.9988389223132 ]
S = [ ...
0.9999787668370 -0.0000003656818 0.0000010063421
-0.0000003656818 1.0000001982183 -0.0000013585088
0.0000010063421 -0.0000013585088 0.9999997856304 ]
Internal Error: Rotation should not scale.
Return code: 248
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