Comments (5)
AdebayoBraimah
commented on July 24, 2024
Hi @whinds , any head way on this issue? I am running into this problem as well.
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whinds
commented on July 24, 2024
No complete solution yet I'm afraid. One trick that helped was to "use mri_convert -c" on the T2 prior to processing, which padded the volume with zeros making transformations and resizing safer.
mri_convert -c -odt float -rt cubic $T2 $T2
Also, in one instance, one of the surface reconstructions failed on a virtual machine was instead able to succeed using the docker method.
My data is 1.0 mm resolution and prone to movement artifacts, so it could also be an underlying issue.
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AdebayoBraimah
commented on July 24, 2024
Understood. Thanks for response @whinds. I will give that a try.
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AdebayoBraimah
commented on July 24, 2024
@whinds Thanks, that seems to have done the trick on some of the images that failed on the first try.
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schuhschuh
commented on July 24, 2024
Hi, sorry for the late reply, but if the resample/cropped t2w-image.nii.gz seems to not cover the full brain region, I would expect this to be an issue with the brain extraction mask. All the above command does is to sample the original (bias corrected) T2w image at the voxels of the supplied brain extraction mask, which is expected to match this image in native space.
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Related Issues (20)
- Surface Reconstruction FAILED, please suggest new parameter values for gaus_curvature and min_width
- Non rigid step failing HOT 2
- exporting surface files (*.dscalar.nii or *.shape.gii) to freesurfer format HOT 1
- Tissue probability maps are not correctly copied
- Error with T1w/T2w maps
- Segmentation error (with docker image) HOT 10
- Surface error under docker image
- Error with dhcp-structural-pipeline:fetal in docker
- Native install on Big Sur
- Segmentation error HOT 3
- Installation difficulties HOT 1
- Calculate curvature in the script process-surfaces-hemisphere
- Infant structural T1 data segmentation HOT 1
- mirtk padding failure for tissue labels
- setup.sh Failure HOT 1
- setup.sh failure
- code version for dHCP release 3? HOT 3
- Pipeline outputs
- docker issue apple silicon chips?
- recon-neonatal-cortex error HOT 8
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