External Email - Use Caution Hi Freesurfer folks,
Has anyone seen this error before with the longitudinal pipeline: Internal Error: Rotation should not scale. Return code: 248 Thanks, Dylan On Tue, Aug 13, 2019 at 8:02 AM Dylan Nielson <dylan.niel...@gmail.com> wrote: > 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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