multi scale brain parcellator install without docker

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pavanc...@gmail.com

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Jan 25, 2021, 11:31:54 AMJan 25
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Hi, 

I am not able to use docker on the machine I am working on. Are there instructions for installing the multiscale brain parcellator without docker? 

Thanks, 
Pavan

Sebastien Tourbier

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Mar 1, 2021, 8:39:48 AMMar 1
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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.
To have an example of the installation steps, you can follow the content of the Dockerfiles which setups the computing environment and installs everything in a Ubuntu 16.04 OS : https://github.com/sebastientourbier/multiscalebrainparcellator/blob/master/environments/Dockerfile and https://github.com/sebastientourbier/multiscalebrainparcellator/blob/master/Dockerfile.

Hope this would help,
Sebastien
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