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aramis-lab / clinica

Software platform for clinical neuroimaging studies
http://www.clinica.run/
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Hippocampus mask unavailable/incompatible #1096

Closed naji-s closed 1 month ago

naji-s commented 4 months ago

Describe the bug I am trying to create left and right Hippocampi masks that would be compatible with Clinica's adni-to-bids (and then to CAPS) converter. Unfortunately though it seems like t1-linear processing is mixed with a cropping that is to my knowledge uses the template ref_cropped_template.nii.gz based on https://github.com/aramis-lab/clinica/blob/37da1cbbed35c5e16877e06b17074c9811a83354/clinica/pydra/t1_linear/t1_linear.py#L11

I have also made a bug issue in clinica-dl here: https://github.com/aramis-lab/clinicadl/issues/537

And including it for clarity, since the original use of masks as part of data prepration is suggested there

My question is that can masks (taken from TamplateFlow be cropped using the reference tempalte I outlined above and they end up being compatible with CAPS data processed through Clinica?

github-actions[bot] commented 1 month ago

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