MCRIB atlas not downloaded to atlas folder

[finnlennartsson]

Hi,

Have installed the feature/MCRIB_integrated branch using the setup.sh script.

Now when I am running.

$mirtk neonatal-segmentation rawdata/sub-PK343/ses-MR1/anat/sub-PK343_ses-MR1_run-001_T2w.nii.gz 40 -atlas MCRIB -d derivatives/neonatal-segmentation_DrawEM_MCRIB/sub-PK343/ses-MR1 -t 10
ls: cannot access '/home/finn/Software/DrawEM/build/MIRTK/Packages/DrawEM/atlases/M-CRIB_2.0/T2': No such file or directory
DrawEM multi atlas  v1.3 (branch version: 820308892ccaceb821a17a8875a6abb3e19bed05)

it cannot find the MCRIB-atlas. In the appropriate location I only have the other atlases

finn@laptop:~/Software/DrawEM/build/MIRTK/Packages/DrawEM$ ls atlases/
ALBERTs  MNI  non-rigid-v2

I have previously downloaded it and have it in another location, but the folder names do no follow your convention, and comparing with the ALBERTs atlas I don't have any gm-posteriors etc etc.

How do I proceed?

Thanks!
Finn

[finnlennartsson]

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

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

[finnlennartsson]

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

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

[lucasfr]

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