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

[ghost]

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

[ghost]

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...