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@cookpa @ntustison
I am running cortical thickness extraction for Brain MRI images (a batch of 4000 MRI images) and encountered a segmentation fault during processing.
The script ran successful…
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Use FSSurface with parcelation to create material segmentation of FSAverage scan to white matter, grey matter, CSF, skull, skin, air
FSaverage has brain segmentation, but it seems skin and skull su…
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When this happens, the resulting YAML is invalid:
```yaml
# Set the threshold value for refining the resulting CSF segmentation tissue mask.
# The default value is 0.95.
# CSF (cerebrospinal flu…
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Add segmentation of grey matter, white matter, csf.
This could possibly allow for:
1) boundary-based-registration of bold to struct instead of ANTs.
2) It could improve skull extraction by removi…
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- make sure that it is the `..._acq-MPRAGE_T1w_reoriented_brain_seg.nii.gz` which contains the final segmentation of gray/white/csf. (and not `_pveseg.nii.gz`). Sample directory `/home/chrispycheng/p…
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Release of the method described in:
https://www.biorxiv.org/content/10.1101/2020.01.14.903559v1
due to community request.
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One issue I will have here:
In `5ttgen hsvs`, by def…
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https://github.com/ANTsX/ANTsPyNet/blob/d39ee8333149a84f6bb72b217419dacfd3872a0d/antspynet/utilities/white_matter_hyperintensity_segmentation.py#L76-L79
causes an error in some installations of pyt…
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Following a conversation with @Lestropie:
At present `5ttgen` algorithms, including `5ttgen hsvs`, usually include the optic chiasma as CSF since its corresponding index is not explicitly assigned t…
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Hello! At some point, we worked with @mareikegrotheer and @bloomdt-uw to implement a pipeline for tractography in neonates/infants (see [this repo](https://github.com/bloomdt-uw/babyafq)), oriented sp…
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Hi,
First of all, I'd like to say that I'm a new user of dcmqi. So I might be doing something wrong, however, let me explain the issue I'm having below:
I have a White Matter Lesion Segmentatio…