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!
> 
>