Dear Freesurfer experts,

I’m running into a problem with mri_robust_template when trying to align multiple T1 images (this is with Freesurfer 6.0.1).

I’m using fmriprep 1.4.1 to preprocess subjects from the OASIS3 dataset (or at least, attempting to). Each subject has 5-7 T1 scans over 3-4 time points, and one of the first steps in fmriprep’s pipeline is to align them all using mri_robust_template. However, the registration is failing every time with the return code -9. I can’t seem to find any indication of what that return code means, so I don’t know what to try to fix.

Does anybody have any idea what “Return code: -9” means?

Thanks, Blaise

RuntimeError: Command: mri_robust_template --satit --fixtp --mov /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30005_ses-d2384_T1w_ras_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30005_ses-d3453_T1w_ras_corrected.nii.gz --inittp 1 --iscale --noit --template sub-OAS30005_ses-d0581_run-01_T1w_template.nii.gz --subsample 200 --lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp5.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp6.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp7.lta Standard output: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

--satit: Will estimate SAT iteratively! --fixtp: Will map everything to init TP! --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30005_ses-d2384_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30005_ses-d3453_T1w_ras_corrected.nii.gz as movable/source volume. Total: 7 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --noit: Will output only first template (no iterations)! --template: Using sub-OAS30005_ses-d0581_run-01_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 '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30005_ses-d2384_T1w_ras_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30005_ses-d2384_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30005_ses-d3453_T1w_ras_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30005_ses-d3453_T1w_ras_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 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz )

[init] ========================= TP 4 to TP 1 ============================== Register TP 4 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz )

[init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz )

[init] ========================= TP 5 to TP 1 ============================== Register TP 5 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz )

-- Original : (1, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter:

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter:

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: -- Original : (1, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) Standard error:

Return code: -9

------------------------------------------------------- Blaise Frederick Associate Professor of Psychiatry/Biophysicist Harvard Medical School/McLean Hospital bbfrederick@mclean.harvard.edu http://www.nirs-fmri.net