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Add 7T T2*w and qT1 in-vivo template + atlas #13

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Nilser3 opened this issue Jun 23, 2023 · 1 comment
Open

Add 7T T2*w and qT1 in-vivo template + atlas #13

Nilser3 opened this issue Jun 23, 2023 · 1 comment

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@Nilser3
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Nilser3 commented Jun 23, 2023

Hi @jcohenadad

It is a template and atlas developed by the CRMBM team, Marseille,
I would like to see the best way for a possibility to implement it in PAM50.

Presented at the ISMRM23 : AMU7T: a 3D qT1 and T2*w high-resolution in vivo template with refined white and gray matter parcellation dedicated to 7T spinal cord MR analyses

Initial remarks:

Alignment with PAM50 template

r = ( 0.175781 x 0.175781 x 0.5 )mm
dim1 110
dim2 90
dim3 224

AMU_7T_1

Atlas labels + Lookup tables for atlas visualization in FSLeyes:

image

@jcohenadad
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jcohenadad commented Jun 24, 2023

@Nilser3 this is great. Happy to provide support, however I would like the SCT core dev team at large to be involved in the support/decisions (ie: the issue is directed at me, but it should be directed to the team).

Few comments:

  • please provide a link to the full ISMRM citation
  • the "Alignment with PAM50 template" would be best assessed by showing the underlying T2* contrast of the PAM50
  • Please indicate where we can find the image files and associated TXT file that contains the atlas labels
  • I suggest opening a branch and PR to discuss this integration

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