Problem with dHCP-structural-pipeline using only T2W image


I am using only T2-w image using the following command:

docker run --rm -t
-u (id−u): (id -g)
-v $PWD/data:/data
biomedia/dhcp-structural-pipeline:latest sub-NYS1553 ses-001 43
-T2 data/sub-NYS1553_ses-001_T2w.nii.gz -t 8

but I am getting Surface, Segmentation and additional errors. I have attached the error files to this message.
sub-NYS1553-ses-001.additional_log.txt (3.6 KB)
sub-NYS1553-ses-001.segmentation_err.txt (12.2 KB)
sub-NYS1553-ses-001.segmentation_log.txt (120.7 KB)
sub-NYS1553-ses-001.surface_err.txt (2.6 KB)
sub-NYS1553-ses-001.surface_log.txt (1.2 KB)

Your help is highly appreciated,

Hi @parinaz,

Are you using dHCP data or your own data? From the file naming in the call above, it looks like the latter? If that is the case, can you give me a bit more information about the T2w scan?

Best wishes,


Hi @lzjwilliams

Thank you very much for your reply. Our data is a 3D image of a 43-week-old infant.
SliceThickness: 0.9
SpacingBetweenSlices: 0.9
EchoTime: 0.072626
RepetitionTime: 3.002
FlipAngle: 90
CoilString: 48HAP
PercentPhaseFOV: 88
EchoTrainLength: 100
AcquisitionMatrixPE: 256
ReconMatrixPE: 256
PixelBandwidth: 488.281

I have also attached the json file of the T2-w image for more information.
sub-NYS1553_ses-001_T2w.txt (1.2 KB)


Hi @parinaz,

There is a version of the dHCP structural pipeline that you can try on non-dHCP style data - it is not part of the official release but we tend to use this version of the pipeline for non-dHCP data within the dept. The main parameter to change is the -recon-from-seg flag when calling the script from the terminal (there is no docker available for this version). The recon-from-seg option allows surface reconstruction from the volumetric segmentation, rather than the typical two-stage surface boundary placement in the official release.

Here is the github repo: GitHub - DevelopingHCP/structural-pipeline at dhcp-v1.1.1, and the recon-from-seg flag: structural-pipeline/ at 7d037fb12d6674938aec93bf664edb7c2d195c49 · DevelopingHCP/structural-pipeline · GitHub

That might help - let me know.


Hi @Logan,

Thank you very much for your reply and the solution that you provided for my situation. I’ve tried so hard to install the desktop version of structural pipeline, but I was not successful. I have attached the setup log.
setup_log.txt (3.8 MB)
I am using macOS Monterey version 12.5 with g+±12/gcc-12 and Xcode 13.4.1
Please give me some suggestions if you have any idea about that.

Thank you for your help,