Continuous map does not have the same shape as the template

[valentin-pinkau]

The continous map of Area Fp1 has a different shape than the corresponding template (97, 115, 97) vs. (193, 229, 193) for the parcellation julich 2.9, space mni152.

[xgui3783]

related: FZJ-INM1-BDA/siibra-python#302

[AhmetNSimsek]

The issue is caused by the template being fetched from a different format, i.e. "neuroglancer/precomputed". siibra-python has the same issue depending on the machine.
After a discussion with @dickscheid, we decided to implement following to siibra-python:

• Predefine the order in which the formats will be used. (1) Nifti 2) Neuroglancer). EDIT: based on comments on #318, the predefinition is already implemented as the loop goes through a list of formats. See ttps://github.com/FZJ-INM1-BDA/siibra-python/blob/01d3d09/siibra/volumes/volume.py#L40-L44
• If the user has not defined a resolution and if neuroglancer decreases the resolution, the user should be warned.

[xgui3783]

I suspect this can also lead to indeterministic behaviours, especially when network is unstable.

see related issue FZJ-INM1-BDA/siibra-python#318

[AhmetNSimsek]

I see. So we need to make sure NG returns the "correct" one. We could define a default resolution_mm to be fetched when it is not provided instead of getting the lowest. What do you think?

[xgui3783]

I see. So we need to make sure NG returns the "correct" one. We could define a default resolution_mm to be fetched when it is not provided instead of getting the lowest. What do you think?

could be a solution.

But this will vary, depending on the voxel resolution of the nifti

[xgui3783]

a fix is being pushed to dev instanced, deployd at https://siibra-api-latest.apps-dev.hbp.eu/. e.g.:

import requests
import nibabel as nib
SIIBRA_API_HOST = "https://siibra-api-latest.apps-dev.hbp.eu"

MNI152_ID="minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
JBA_29_ID="minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290"
regions = ["Area hOc1 (V1, 17, CalcS) - right hemisphere", "Area Fp1 (FPole) - right hemisphere", None]
endpoints = ["/v3_0/map/statistical_map.nii.gz", "/v3_0/map/labelled_map.nii.gz"]
for endpoint in endpoints:
    for region in regions:
        if region is None and endpoint == "/v3_0/map/statistical_map.nii.gz":
            continue
        
        query_param = {
            'space_id': MNI152_ID,
            'parcellation_id': JBA_29_ID,
        }

        if region:
            query_param['region_id'] = region
        
        resp = requests.get(f"{SIIBRA_API_HOST}{endpoint}", params=query_param)
        resp.raise_for_status()
        with open("boo.nii.gz", "wb") as fp:
            fp.write(resp.content)
        nii = nib.load("boo.nii.gz")
        assert nii.get_fdata().shape == (193, 229, 193)

I will post another update when the changes hits prod.

[xgui3783]

I wanted to close this issue, but upon further testing the issue is not yet resolved from upstream siibra-python.

see FZJ-INM1-BDA/siibra-python#368 for the continuation of the issue report.

What this means for siibra-api: you may continue to see masks/statisticalmap/labelled map to have different dimension than the template.

I will post an update when there are new developments.

[xgui3783]

should be fixed by https://github.com/FZJ-INM1-BDA/siibra-api/releases/tag/v0.3.6