New atlas: Subject-space DKT (recon-all FreeSurfer)

[ftadel]

IntrAnat: @ftadel
1) BrainVisa ontology: Add storage space for FreeSurfer file: mri/aparc.DKTatlas+aseg.mgz 1) ImageImport: Import mri/aparc.DKTatlas+aseg.mgz into BrainVisa database 1) locateElectrodes: Add subject-space DKT atlas to .csv generation 1) If subject-space DKT not available, use a MNI-based DKT

f-tract server: @manikbh 1) Identify list of patients that do not have aparc.DKTatlas+aseg.mgz:

• Patients on which the older FreeSurfer installations (FreeSurfer 5.3 or FreeSurfer 6) failed
• Patients processed successfully with older versions of FreeSurfer which did not include DKTatlas (FreeSurfer < 6.0) 1) Install FreeSurfer 7.1 1) Re-run all these patients with FreeSurfer 7.1 1) Run the scripts to generate the HCP-MMP1 atlas: https://github.com/ftadel/IntrAnat/issues/7 1) Copy the freesurfer output folders (ftract_transfer) 1) Import the FreeSurfer output folder for all these subjects into the BrainVISA/IntrAnat database 1) Re-generate the CSV for all these patients

[ftadel]

Import of the subject-space DKT and HCP-MMP1: https://github.com/ftadel/IntrAnat/commit/ca6ef826a5adb19ac2cd81901e1c4ad661052b79

Display of DKT and HCP-MMP1 in locateElectrodes: https://github.com/ftadel/IntrAnat/commit/020cdd204eecdf36f5608288e84ba99c9895fbe7

[ftadel]

DKT and MNI-DKT included in the CSV files: https://github.com/ftadel/IntrAnat/commit/9eabffbf3c5d80a96f1c03be42ecc95fc2cb3d93

ftractTransfer moved to github and adapted for updating DKT+HCP: https://github.com/ftadel/IntrAnat/commit/794be5f57d6ce490353e9549664aef9b47ba1a30

Batch FreeSurfer import: https://github.com/ftadel/IntrAnat/commit/3bd178e7d881f253b5203fd5cf765c799e43dff0

Batch CSV generation: https://github.com/ftadel/IntrAnat/commit/6c3bc39cfeee9127de68280052a9c7f013c6f55f

IntrAnat side finished, removing @ftadel from the assignees.