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
2. ImageImport: Import mri/aparc.DKTatlas+aseg.mgz into BrainVisa database
3. locateElectrodes: Add subject-space DKT atlas to .csv generation
4. 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)
2. Install FreeSurfer 7.1
3. Re-run all these patients with FreeSurfer 7.1
4. Run the scripts to generate the HCP-MMP1 atlas: New atlas: HCP-MMP1 subject space (FreeSurfer custom commands) #7
5. Copy the freesurfer output folders (ftract_transfer)
6. Import the FreeSurfer output folder for all these subjects into the BrainVISA/IntrAnat database
7. Re-generate the CSV for all these patients

[ftadel]

Import of the subject-space DKT and HCP-MMP1: ca6ef82

Display of DKT and HCP-MMP1 in locateElectrodes: 020cdd2

[ftadel]

DKT and MNI-DKT included in the CSV files: 9eabffb

ftractTransfer moved to github and adapted for updating DKT+HCP: 794be5f

Batch FreeSurfer import: 3bd178e

Batch CSV generation: 6c3bc39

IntrAnat side finished, removing @ftadel from the assignees.