Hello,
I’m using fmriprep version 1.3.0 on a subject (who’s passed BIDS validation), yet freesurfer’s recon-all keeps failing.
The last portion of the recon-all-rh.log is provided
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
77731 ambiguous faces found in tessellation
segmenting defects...
54 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 14 into 11
-merging segment 23 into 11
-merging segment 28 into 11
-merging segment 29 into 11
-merging segment 32 into 30
-merging segment 42 into 41
-merging segment 44 into 43
47 defects to be corrected
0 vertices coincident
reading input surface /N/dc2/scratch/dlevitas/fMRI_data/std/bids/derivatives/freesurfer/sub-1003/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -8.5385 (-4.2693)
-vertex loglikelihood: -6.1084 (-3.0542)
-normal dot loglikelihood: -3.3622 (-3.3622)
-quad curv loglikelihood: -5.8410 (-2.9205)
Total Loglikelihood : -23.8501
CORRECTING DEFECT 0 (vertices=10, convex hull=15, v0=68)
After retessellation of defect 0 (v0=68), euler #=-38 (107121,317176,210017) : difference with theory (-44) = -6
CORRECTING DEFECT 1 (vertices=87, convex hull=114, v0=1031)
After retessellation of defect 1 (v0=1031), euler #=-37 (107170,317370,210163) : difference with theory (-43) = -6
CORRECTING DEFECT 2 (vertices=1097, convex hull=164, v0=4189)
normal vector of length zero at vertex 107406 with 3 faces
After retessellation of defect 2 (v0=4189), euler #=-36 (107199,317534,210299) : difference with theory (-42) = -6
CORRECTING DEFECT 3 (vertices=204, convex hull=211, v0=6243)
After retessellation of defect 3 (v0=6243), euler #=-35 (107258,317801,210508) : difference with theory (-41) = -6
CORRECTING DEFECT 4 (vertices=304, convex hull=72, v0=6411)
After retessellation of defect 4 (v0=6411), euler #=-34 (107275,317885,210576) : difference with theory (-40) = -6
CORRECTING DEFECT 5 (vertices=5, convex hull=31, v0=11827)
After retessellation of defect 5 (v0=11827), euler #=-33 (107276,317895,210586) : difference with theory (-39) = -6
CORRECTING DEFECT 6 (vertices=81, convex hull=73, v0=14197)
After retessellation of defect 6 (v0=14197), euler #=-32 (107288,317962,210642) : difference with theory (-38) = -6
CORRECTING DEFECT 7 (vertices=21, convex hull=49, v0=14349)
After retessellation of defect 7 (v0=14349), euler #=-31 (107292,317992,210669) : difference with theory (-37) = -6
CORRECTING DEFECT 8 (vertices=253, convex hull=79, v0=15446)
After retessellation of defect 8 (v0=15446), euler #=-30 (107327,318137,210780) : difference with theory (-36) = -6
CORRECTING DEFECT 9 (vertices=47, convex hull=54, v0=16771)
After retessellation of defect 9 (v0=16771), euler #=-29 (107338,318191,210824) : difference with theory (-35) = -6
CORRECTING DEFECT 10 (vertices=74, convex hull=108, v0=18591)
After retessellation of defect 10 (v0=18591), euler #=-28 (107375,318353,210950) : difference with theory (-34) = -6
CORRECTING DEFECT 11 (vertices=34006, convex hull=4436, v0=19489)
normal vector of length zero at vertex 123234 with 0 faces
vertex 123234 has 0 face
XL defect detected...
Numerical result out of range
Linux c41 3.10.0-862.14.4.el7.x86_64 #1 SMP Fri Sep 21 09:07:21 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-1003 exited with ERRORS at Wed Apr 17 21:17:10 UTC 2019
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
For reference, the fmriprep command I use is
unset PYTHONPATH; singularity run -B $HOME/templateflow:/opt/templateflow $HOME/*fmriprep*img \
$data_dir $data_dir/derivatives \
participant \
--participant-label $s \
--fs-license-file $HOME/bids_stuff/license.txt \
--ignore slicetiming \
--use-aroma \
--aroma-melodic-dimensionality 100 \
--output-space T1w fsnative template fsaverage5 \
--write-graph \
--nthread $nthreads \
--omp-nthreads 2 \
--stop-on-first-crash \
--resource-monitor \
--low-mem \
--mem_mb $mem_mb \
--use-plugin $HOME/plugin_${s}.yml \
-w $data_dir/derivatives
I’m unsure if I should just disable the freesurfer processing for this subject, or if there is some fix for this issue?
Thanks,
Dan
