External Email - Use Caution        

Thanks for taking a look at this Martin. I've uploaded the files to my google drive, you should be able to find them here:
https://drive.google.com/open?id=1GmdgXr0kFP10YYw6Wk8Vio7_dcZHNYL4

I've put each subject in their own directory along with the input files, the original command, and the command edited to just use local paths so that you can just run it from that directory. 

Thanks again and let me know if there's anything else I can do to help diagnose this issue.

-Dylan

On Wed, Aug 14, 2019 at 2:11 PM Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Hi, 
To debug this, I would need the 4 input images and the command. Of course the error would need to also come up when using those images.

Best Martin


Am 14.08.2019 20:01 schrieb "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>:

I have not seen it before; I've cc'ed Martin in case he has seen it.
Have you checked the underlying data to make sure that there are no
artifacts, etc?

On 8/13/19 8:02 AM, Dylan Nielson wrote:
>
>         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 didnot  converge !!
> * WARNING: TP 3 to 1 didnot  converge !!
> * WARNING: TP 4 to 1 didnot  converge !!
>
> Inputrotation's max deviation fromrotation  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 )
> Standarderror:
> 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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