MCRIB atlas not downloaded to atlas folder about drawem HOT 5 OPEN

I am having a similar issue.
Also hoping for a speedy solution...

from drawem.

Have downloaded and built DrawEM after MCRIB was merged into the master-branch. As before the $DRAWEMDIR/atlases does not contain any MCRIB-atlas.

However, from the configuration-script $DRAWEMDIR/parameters/MCRIB/configuration.sh I can set the relevant paths

export ATLAS_T2_DIR=$DRAWEMDIR/atlases/M-CRIB_2.0/T2
export ATLAS_TISSUES_DIR=$DRAWEMDIR/atlases/M-CRIB_2.0/tissues
export ATLAS_SEGMENTATIONS_DIR=$DRAWEMDIR/atlases/M-CRIB_2.0/segmentations

I have done this manually (or actually in first play-around just making the equivalent folder structure in $DRAWEMDIR/atlases/M-CRIB_2.0 and filling it with the relevant files from the M-CRIB_2.0 atlas.)

I am still not there and have some questions.

• The M-CRIB_2.0 atlas does not contain a any tissue segmentations.
  Can these be found somewhere?
  If not, would it be possible to generate these? I guess again from one of the variables in the $DRAWEMDIR/parameters/MCRIB/configuration.sh (like $ALL_LABELS_TO_TISSUE_LABELS) and using mirtk padding command? However, I am not so used to using this. Advice would be appreciated!

• I would be good to get confirmed which T2 you are expecting (raw or preprocessed).

Thanks in advance!
Finn

from drawem.

Hello Finn,
did you manage to resolve this? I am currently dealing with the same problem and would be thankful for any advice :)
Best,
Andrea

from drawem.

Hi Andrea,

No, not yet. Have been in contact with Antonios @amakropoulos, but as of until some months ago, the licensing thing had not yet been completely resolved.

Cheers
Finn

from drawem.

Hello,
It seem we need to cross our fingers for the speedy resolution then :) and to come up with some alternative solution until then.
Thanks again.

Have a lovely day,
Andrea

from drawem.