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 CautionHi 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 CautionI 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:
- 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
- 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