Re: [Freesurfer] mris_convert segmentation fault on R hemisphere aparc.a2009s only?

yup, sounds good. Good luck Bruce On Thu, 22 Aug 2019, Damion V Demeter wrote:

External Email - Use Caution

Hi Bruce,

I have been doing some investigating on our side and I believe the issue may have to do with something in our environment. It appeared to happen across systems, but we are not experiencing the error on another system. I am trying to identify what is different/went wrong. If it can't be cleared up on our side after a few more tests, I will upload and revive this thread, if that's ok. (I will also get the env differences).

I appreciate your help! Damion

On Thu, Aug 22, 2019 at 1:39 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Damion

  you can upload them to our ftp
  site

  https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

  cheers
  Bruce

  On
  Sun, 18 Aug 2019, Damion V Demeter wrote:

  >
  >         External Email - Use Caution        
  >
  > Hi Bruce, 
  >
  > My apologizes, I just saw this reply because I didn't realize
  I had the list
  > on digest mode. I would very much appreciate your help!
  How/where should I
  > upload the files? 
  >
  > Thank you!
  > Damion
  >
  >
  > 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 pipeli
  > ne
  > > 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 wer
  > e
  > > fully processed fine without error (over 100 of them) and
  are from the sam
  > e
  > > group (all scanner and acquisition settings identical). Here
  is the
  > > segmentation fault error line:
  > >
  > > FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 294:
  46979 Segmentati
  > on
  > > fault      mris_convert --annot
  > > "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot
  > >
  "$FreeSurferFolder"/surf/"$hemisphere"h.white"$AtlasSpaceFolder"/"$NativeF
  > older"/"$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, howeve
  > r,
  > > 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!
  > >
  > >
  >
  > -----
  > Damion Demeter, MA
  > Doctoral StudentUT Austin | Cognitive Neuroscience
  > DCN Lab
  >
  >