dhcp-structural-pipeline

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recon-neonatal-cortex error

8

Hello, I am trying to run the pipeline on infants from the Baby Connectome Project. Most, but not all participants receive an error during surface analysis. I have copied the...

alexamousley

code version for dHCP release 3?

3

What version of this code was used for dHCP release 3? @jcupitt do you know?

maxpietsch

setup.sh Failure

1

I 'm tryng to set up the dhcp pipeline but i have a configuration problem about the installation as cited above : make /usr/src/structural-pipeline -DMIRTK_DIR=/usr/src/structural-pipeline/build/MIRTK/build/lib/cmake/mirtk -DVTK_DIR=/usr/src/structural-pipeline/build/VTK/build -DITK_DIR=/usr/src/structural-pipeline/build/ITK/build -DCMAKE_CXX_COMPILER=/usr/bin/g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5 :...

EmilioIppoliti

Hi, I’m trying to run the docker version of the pipeline on a mac and it seems to go well until the dof folder starts get filled (don’t know which...

jottinog

Infant structural T1 data segmentation

1

Hi, I would like to run developing HCP pipeline to perform segmentation of neonatal T1 scans. I know it surely works on T2 data , I would like to know...

rosella1234

Dear all, I just downloaded the dHCP pipeline from docker. I noticed the output format for the surface reconstruction files is Gifti. I am used to vtk files. Do you...

fleurgaudfernau

Segmentation error

4

Any ideas on how to fix this? thanks!

ajdneuro12

Non rigid step failing

2

Hi all, Thanks for sharing the pipeline. I am using the most recent docker version on a mac and it is failing at this step: usr/src/structural-pipeline/build/MIRTK/Packages/DrawEM/scripts/tissue-priors.sh T2w 40 non-rigid-v2 1...

ajdneuro

Hello, When running the setup.sh file on Ubuntu 18.04 I get the following error during the VTK part: CMake Error at /dhcp-structural-pipeline/build/VTK/CMake/ExternalData.cmake:1005 (message): Object MD5=58c536bccfe18a4dc4d157f35e821489 not found at: http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=58c536bccfe18a4dc4d157f35e821489&algorithm=MD5 ("HTTP...

CST333

Error messages from the .log and .err respectively: mirtk padding segmentations/{99988811}.nii-session1_tissue_labels.nii.gz segment ations/{99988811}.nii-session1_tissue_labels.nii.gz masks/{99988811}.nii-session 1-labels.nii.gz 2 1 4 0 : failed IOError: Cifst ream::Open: Failed to open file segmentations/{99988811}.nii-session1_tissue_lab els.nii.gz...

pkashya