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
>
>