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Hello FreeSurfer Developers,
I am running recon-all with the -localGI option to compute local gyrification index (LGI). Across multiple subjects from the same dataset, the pipeline fails at different stages. Although the failure points differ, all errors appear to be related to *posterior fossa inclusion (cerebellum or dura)* in the filled or white matter volumes.
Below I describe two distinct failure patterns observed in different subjects.
*1) What I am trying to accomplish* I am running recon-all with -localGI to compute local gyrification index (LGI). The error occurs only in a specific subject.
*2) Command I ran*
recon-all -i {name of the nii files}.nii -s {name of the new file} -sd {directory of the new file} -all
*3) Exact error output*
*1) Failure pattern 1: filled volume stage*
(*Subjects: SPR_023_gi, SPR_024_gi, SPR_025_gi, SPR_037_gi*)
In these subjects, recon-all fails early at the mri_fill stage with the following error message:
error: Please check filled volume. Cerebellum may be included.
*2) Failure pattern 2: topology defect correction stage*
*(1) Topology Abort*
(*Subject: SPR_039_gi, SPR_052_gi, SPR_070_gi, SPR_071_gi, SPR_078_gi, ,SPR_082_gi, SPR_084_gi, SPR_085_gi, SPR_092_gi*)
1. SPR_039_gi
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
CORRECTING DEFECT 101 (vertices=11842, convex hull=2982, v0=103450)
Abort
The run terminates with:
recon-all -s SPR_039_gi exited with ERRORS
2. SPR_052_gi In an additional subject (SPR_052_gi), recon-all also aborts during topological defect correction: CORRECTING DEFECT 26 (vertices=16843, convex hull=2967, v0=19098) Abort
3. SPR_070_gi
CORRECTING DEFECT 11 (vertices=20829, convex hull=3275)
Abort
4. SPR_071_gi
CORRECTING DEFECT 83 (vertices=15893, convex hull=2782, v0=123875)
Abort
5. SPR_078_gi
CORRECTING DEFECT 0 (vertices=54094, convex hull=2051, v0=0)
Abort
6. SPR_082_gi
CORRECTING DEFECT 43 (vertices=13775, convex hull=2607, v0=41288)
Abort
7. SPR_084_gi
CORRECTING DEFECT 16 (vertices=14335, convex hull=4350, v0=21574)
Abort
8. SPR_085_gi
CORRECTING DEFECT 0 (vertices=18840, convex hull=3104, v0=591)
Abort
9. SPR_092_gi
CORRECTING DEFECT 19 (vertices=9080, convex hull=3587, v0=17615)
Abort
(2) Topology segfault(signal11)
(*Subject: SPR_058_gi, SPR_063_gi,*)
1. SPR_058_gi An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz.
CORRECTING DEFECT 38 (vertices=15899, convex hull=3154) Command terminated by signal 11
2. SPR_063_gi
CORRECTING DEFECT ...
Command terminated by signal 11
*(3) LGI computation stopped due to topological defects*
*(Subject: SPR_079_gi, SPR_136_gi)*
1. SPR_079_gi
WARNING -- Problem for vertex iV = 20401, lGI value is aberrantly high (lGI=47.0556)...
This may be caused by topological defects, check mris_euler_number on the pial surface.
ERROR: compute_lgi did not create output file 'rh.pial_lgi.asc'
2. SPR_136_gi
ERROR: compute_lgi did not create output file 'lh.pial_lgi.asc'
*4) FreeSurfer version*
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
*5) Platform*
OS: Ubuntu 20.04.1 LTS
uname -a: Linux climb 5.15.0-139-generic #149~20.04.1-Ubuntu SMP Wed Apr 16 08:29:56 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
*6) recon-all.log*
all files are attached to this email.
Thank you very much for your time and help.
Best regards,
Hyowon Ju.