Surface error under docker image

[weilancys]

trafficstars

Hi,

I was trying to use the pipeline script on images of 40 weeks old and got this error:

xxx@host:~$ docker run --rm -t -u $(id -u):$(id -g) -v $PWD/data:/data biomedia/dhcp-structural-pipeline:latest subject1 session1 40 -T1 data/sub-CC00060XX03_ses-12501_T1w.nii.gz -T2 data/sub-CC00060XX03_ses-12501_T2w.nii.gz -t 8
dHCP pipeline v1.1
Subject:     subject1
Session:     session1 
Age:         40
T1:          sub-CC00060XX03_ses-12501_T1w.nii.gz
T2:          sub-CC00060XX03_ses-12501_T2w.nii.gz
Directory:   /data 
Threads:     8
Minimal:     1
Warning: Number of threads>1: This may result in minor reproducibility differences


/usr/src/structural-pipeline/dhcp-pipeline.sh subject1 session1 40 -T1 data/sub-CC00060XX03_ses-12501_T1w.nii.gz -T2 data/sub-CC00060XX03_ses-12501_T2w.nii.gz -t 8
----------------------------
running segmentation pipeline
/usr/src/structural-pipeline/scripts/segmentation/pipeline.sh /data/workdir/subject1-session1/T2/subject1-session1.nii.gz subject1-session1 40 -d /data/workdir/subject1-session1 -t 8
-----------------------
running additional pipeline
/usr/src/structural-pipeline/scripts/misc/pipeline.sh subject1-session1 40 -d /data/workdir/subject1-session1 -t 8
-----------------------
running surface pipeline
/usr/src/structural-pipeline/scripts/surface/pipeline.sh subject1-session1 -d /data/workdir/subject1-session1 -t 8
Pipeline failed: see log files /data/logs/subject1-session1.surface.log /data/logs/subject1-session1.surface.err for details

In the log directory, I found 6 log files:

xxx@host:~/data/logs$ ls
subject1-session1.additional.err    subject1-session1.segmentation.log
subject1-session1.additional.log    subject1-session1.surface.err
subject1-session1.segmentation.err  subject1-session1.surface.log

the subject1-session1.surface.log file ends with this line failed: see log files logs/subject1-session1.surface.R-hemisphere.log , logs/subject1-session1.surface.R-hemisphere.err for details there's no subject1-session1.surface.R-hemisphere.err in the logs directory.

I've attached a zipped logs directory to this issue. logs.zip

Please help, thanks.

[Gitnew1]

I have the same problem.Have you solve it?

[weilancys]

I have the same problem.Have you solve it?

sorry this was posted a long time ago. I don't remember much about the problem now. It was probably not solved and we sought other ways to address our problem.