Hi Damion
if you upload the relevant files so that we can replicate this we will
fix it
cheers
Bruce
On Wed, 14 Aug 2019, Damion V Demeter wrote:
External Email - Use Caution
I am having an issue processing some of my subjects through the HCP pipeline
and have no idea what this error means. If anyone could help out, I'd
appreciate it! Here is all the info:
1. Some (not all) of my subjects are getting a segmentation fault error
during the post-freesurfer step of the HCP pipeline. Previous subjects were
fully processed fine without error (over 100 of them) and are from the same
group (all scanner and acquisition settings identical). Here is the
segmentation fault error line:
FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 294: 46979 Segmentation
fault mris_convert --annot
"$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot
"$FreeSurferFolder"/surf/"$hemisphere"h.white"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.
label.gii
2. I have narrowed down this error further and have found that it only
happens on the right hemisphere aparc.a2009s file. I have manually run the
command above for the left and right hemisphere files separately as a test,
and the L hemisphere files complete without fail. The R hemisphere, however,
always gets this segmentation fault.
This only occurs on certain subjects, but all the files this command is
using look good and error free. All previous steps appeared to finish
without fail and all expected files were written and can be opened (I'm 99%
sure...I might have missed something). I am at a complete loss at how to
troubleshoot this further or fix this error. Does anyone have any ideas or
solutions?
Thank you!
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