dhcp-structural-pipeline

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Hi I was trying to run the dhcp-structural-pipeline, and I noticed the command in process-surfaces-hemisphere: `run mirtk calculate $outvtk/$hs.curvature.vtk -mul -1 -scalars Curvature -out $outvtk/$hs.curvature.vtk` Why was the curvature multiplied...

zrk8635

Hi, I would really like to get the pipeline running natively. I am on Big Sur 11.2.3. The install is crashing building VTK. I am attaching the log. Thanks for...

ajdneuro

Hi, I was trying to use the dhcp-structural-pipeline:fetal (in docker) to segment fetal brain. I ran the command as follows: `xuxinyi@DESKTOP-LFK9GOB:/mnt/c/Users/lenovoM425/Desktop/segment-fetal$ docker run dhcp-segmentation-pipeline:fetal 25w1wpp.nii.gz 25 25w1wpp.nii.gz does not exist!...

Thea-Eddie-Amy

Surface error under docker image

2

Hi, I was trying to use the pipeline script on images of 40 weeks old and got this error: ```bash xxx@host:~$ docker run --rm -t -u $(id -u):$(id -g) -v...

weilancys

Segmentation error (with docker image)

10

 [subject1-session1.additional.log](https://github.com/BioMedIA/dhcp-structural-pipeline/files/5423642/subject1-session1.additional.log) I want to perform cortical segmentation of neonatal brain. I was able to successfully install the docker image and I tested two nifti files (preterm and term subjects)...

anisha1807

Hi, When I created the T1w/T2w maps. I found an error and I had to replace the header of the registered T1w by the one of the T2w to create...

mblesac

Hi, When I run the pipeline (locally) with the -additional flag the obtained tissue probability maps for the gm, csf and wm are the same, all of them are the...

mblesac

exporting surface files (*.dscalar.nii or *.shape.gii) to freesurfer format

1

Hi, I would need some help for the interpretation of the curvature and sulcal maps coming out of the pipeline. I would like to convert them to FreeSurfer format (*h.curv,...

urrand

SurfaceRecon - removing_intersections - Exception: Failed to resolve self-intersections

5

After looking in the workdir, it appears the file **t2w-image.nii.gz** is not the same as the original T2 which was used as input to the pipeline.  Original Image: Image...

whinds

Segmentation error

2

Hi all, Thank you for sharing this pipeline. I am trying to run it on my neonate data (infants scanned within 3 months of birth). I formatted my data to...

ajdneuro12