Connectome access

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  • 06/08/2018 at 4:12 PM #4873
    ajtwohy
    Participant

    Hi there,

    My team and I are using Lead-DBS to map standardized DTI connectomes onto patients with Parkinson’s Disease and Obsessive Compulsive Disorder. We can successfully generate VTA fields from our data set. However, our host organizations server has blocked your website (we’ve contacted the IT department and have been informed the issue will not be resolved), so we are unable to proceed without the group connectomes. In addition, we can only use Matlab through the organization, and thus through their fire walls.

    We’re wondering if they’re is an alternative way to download the group connectome datasets other than the lead-DBS gui. The only way we can access the Lead-DBS website if when we are off-site, and the only way we can run Matlab is onsite (and thus the server blocks the downloads called by the lead-dbs gui).

    Thank You,
    Alex

    06/08/2018 at 6:39 PM #4874
    ningfei
    Keymaster

    Hi Alex,

    Which group connectome from the meu do you need? I I can give another download link later.

    Best,
    Ningfei

    06/08/2018 at 8:04 PM #4875
    ajtwohy
    Participant

    Thank you for your quick reply,

    If I could get the 4 structural group connectomes (20 subjects Gibbs-tracker, 169 NKI subjects Gibbs-tracker, 32 Adult Diffusion HCP subjects GQI, and the 90 PPMI PD-patients GQI) I would be in really great shape.

    Thank you so much!

    Alex

    06/08/2018 at 8:29 PM #4876
    ningfei
    Keymaster

    As below:

    20 subjects Gibbs-tracker (Horn 2013)
    169 NKI subjects Gibbs-tracker (Horn 2016)
    32 Adult Diffusion HCP subjects GQI (Horn 2017)
    90 PPMI PD-patients GQI (Ewert 2017)

    Best,
    Ningfei

    06/18/2018 at 4:05 PM #4940
    ajtwohy
    Participant

    Hello Ningfei,

    Thank you so much for your links. I can happily report I have the entire pipeline up and running now.

    I do have a follow-up question: My team and I are trying to replicate your connectivity process in FSL (specifically using the bedpostx and probetrackx processes). We’ve been trying to use the JHU ICBM normative DTI Atlas for this replication (we don’t have DTI data for our own study because we are looking at patients post-electrode implantation), but it lacks the bval and bvec data necesarry to run the analysis. We were also hoping to use your data in the FSL pipeline, but your connectome files are in .mat format and can’t be used in the FSL environement. Our questions are how you condensed the connectome datasets into .mat files, and if there was a way to use your connectomes in FSL.

    Thank you,

    Alex

    07/09/2018 at 5:17 PM #5060
    area51
    Participant

    Once downloaded where should these connectome folders be placed on the hard drive?

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Viewing 6 posts - 1 through 6 (of 6 total)
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