Hi Pavan!
Could you use singularity? If yes, you could run
connectomemapper3 which provides a singularity image (
"singularity pull library://connectomicslab/default/connectomemapper-bidsapp:latest"). Here the documentation page on how to use it:
https://connectome-mapper-3.readthedocs.io/en/latest/runonhpc.html. You can run only the anatomical pipeline (which corresponds to the multi-scale brain parcellator pipeline) by providing only the anatomical pipeline configuration file i.e.:
$ singularity run --containall \
--bind ${localDir}:/bids_dir --bind ${localDir}/derivatives:/output_dir \
library://connectomicslab/default/connectomemapper-bidsapp:latest \
/bids_dir /output_dir participant --participant_label 01 02 03 \
--anat_pipeline_config /bids_dir/code/ref_anatomical_config.ini \
--fs_license /bids_dir/code/license.txt \
--number_of_participants_processed_in_parallel 3
The configuration file ref_anatomical_config.ini can be generated by the graphical user interface (cmpbidsappmanager).
If you cannot also use singularity, then you will have to install FSL 5.0.9 and Freesurfer 6.0.1 manually, clone the github repository, and then from the cloned repository, install the conda environment with dependencie of multi-scale brain parcellator and install multi-scale brain parcellator with "python setup.py install" inside the created conda environment.
Hope this would help,
Sebastien