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 <fis...@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 > > > >
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