Extract Lausanne 2008 ROIs outside Connectome Mapper pipeline?

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Katelyn Arnemann

Jul 5, 2018, 3:47:51 PM7/5/18
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Hi folks,

I am interested in using the Lausanne 2008 ROIs for analysis on PET data. I have already run Freesurfer on all of the MRIs, and I am wondering if there is a direct way to extract the further subsamplings (e.g. 500 ROIs) without having going through the Connectome Mapper pipeline (e.g. setting up all of the directories, etc).

When answering, please assume that I am not a Freesurfer or Connectome Mapper expert, but I can run basic commands with Freesurfer and FSL and know Python (e.g. nibabel).

Thanks for any help!

Morgan Hough

Dec 18, 2018, 10:21:45 AM12/18/18
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Hi Katelyn,

Did you get any reply on this? Did you already ask the same question on the FreeSurfer list? I will check there too.



Ariana Familiar

Jan 13, 2020, 1:59:07 PM1/13/20
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Hi Katelyn & Morgan,

Any update on this? I'm interested using the ROIs outside of the Connectome Mapper as well.


Sebastien Tourbier

Jan 14, 2020, 3:48:51 AM1/14/20
to cmtk-users
Hi all,

Yes it is now possible. The Lausanne2008 parcellation pipeline has been made also standalone and released as a BIDS App named multiscalebrainparcellation last year. Github: https://github.com/sebastientourbier/multiscalebrainparcellator

This means that you would need to have Docker installed on your computer and a dataset organized following the BIDS standard (https://bids.neuroimaging.io) which includes a T1w image.

Data already processed with FreeSurfer?

The multiscalebrainparcellator generate outputs following the BIDS derivatives specifications such that Freesurfer outputs are generated in <bids_dataset_root_directory>/derivatives/freesurfer/sub-<participant_label>. See https://multiscalebrainparcellator.readthedocs.io/en/latest/outputs.html for more details.

If you have your data already processed with FreeSurfer, you can move/copy each Freesurfer subject folder (the folder which contains the mri/, label/, surf/, ...) into <bids_dataset_root_directory>/derivatives/freesurfer/sub-<participant_label> such that the multiscalebrainparcellator will not perform at run Freesurfer recon-all again.


Ariana Familiar

Jan 14, 2020, 1:59:35 PM1/14/20
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Thank you Sebastien! This is very helpful.
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