khanlab / hippunfold

BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)

https://hippunfold.readthedocs.io

khanlab/hippunfold Issues

WorkflowError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/Snakefile, line 7: Config file must be given as JSON or YAML with keys at top level.
Updated 3 days ago2
expanded DG
Closed 7 days ago1
Alternative simple CLI for hippunfold
Updated 16 days ago
atlas2parc
Updated 16 days ago
anterior-posterior subdivisions option
Updated 16 days ago
Docker untar permissions
Closed 17 days ago2
UID Issue on Linux
Closed 17 days ago2
Default Atlas
Updated 14 days ago3
transform the native hippocapus metrics to the unfolded space
Closed 2 months ago4
Segmentation Inaccuracies with degenerated hippocampi
Updated 2 months ago21
Incomplete hippocampal volumes extraction
Closed 2 months ago1
Hippunfold errors out at 46%
Closed 3 months ago3
Hippunfold on pediatric data?
Updated a month ago3
errors while running hippunfold with slurm & snakemake
Closed 2 months ago4
QC-related question
Closed 4 months ago3
How to know when subjects are fully processed?
Closed 4 months ago1
another error on the ds002168 example dataset
Closed 5 months ago2
Sampling functional data for the dentate gyrus
Closed 8 months ago2
Error running ds002168 (example) subject: Potentially with symbolic links?
Closed 2 months ago15
Question: QC/unetf3d_dice.tsv
Closed 9 months ago1
Tutorial for transforming BigBrain to MNI
Closed 9 months ago3
sample functional data along surface
Closed 10 months ago9
Naming of histologyReference2023
Closed 9 months ago3
label.gii and dlabel.nii files for subfields are corrupt in v1.3.0+
Closed 10 months ago
process HCP fmri on hippunfold results
Closed 10 months ago2
zero value vertices on dentate gyrus
Closed 10 months ago4
DG surface contains self-intersection
Closed 10 months ago6
small bug present when visualizing with freeview
Closed 10 months ago1
Converting inner/outer surface files to WM and pial format in Freesurfer
Closed a year ago3
Bug in crop native space
Closed a year ago1
Cyclic dependency on rule warp_gii_to_native.
Closed a year ago11
Windows docker instructions
Closed 2 years ago1
missing subfield.dlabel.gii outputs
Closed 2 years ago2
resample_hippdwi_to_template container missing
Closed 2 years ago1
Add DAG generation to a github action
Updated 2 years ago
Summary statistics of the surface metrics
Updated 2 years ago3
unfolded DG template not rectangular
Closed 2 years ago
run inference duration
Closed 2 months ago4
long staging
Updated 2 years ago1
Cryptic error given when running hippunfold before `hippunfold_download_models` is run
Closed 2 years ago3
`.snakebids` file not found
Closed 2 years ago10
group-level analysis broken
Closed 2 years ago
test-time augmentation actually disabled by default
Closed 2 years ago
Total Intracranial volume estimates
Updated 2 years ago2
simplified outputs by concatenating label-hipp/dentate
Updated 2 years ago2
error with tempmodel/nnUNet
Closed 2 years ago8
add better support for conda
Updated 15 days ago2
hippunfold simple use case returns error
Closed 2 years ago20
error in rule run_inference
Closed 2 years ago7
singularity run not working
Closed 2 years ago3