Cannot find Brain T1 NIFTI files

Trang Minh Nguyen

Hi,

We already dispensed the bulk data files and I was able to access the Bulk directory. However, when I go to Brain MRI > T1 directory, I only see FreeSurfer files in the zip files, not the NIFTI files. Can you tell me where I can access T1 NIFTI files for brain MRI? Thank you!

Comments

3 comments

Date Votes
  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Trang,

    to search for bulk fields, one way is to find the field_id from UKB Showcase and then use the UKB-RAP filters.   See https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/accessing-data/accessing-bulk-data 

    For example, if you search Showcase for Nifti it should show that Field 20252 is T1 structural brain images - NIFTI.  

    Then filter for field_id : 20252 across the entire project.  The results show the UKB-RAP folder structure.   (eid values hidden).

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  • Comment author
    Trang Minh Nguyen

    Thank you, I see that only some zip files have the nii.gz files. If I'm interested in using those NIFTI files, do I have to download everything to my local workspace to unzip and do further processing in python?

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  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Trang,

    to work with the files, I think you will need to use either the CLI or the Ttyd or the JupyterLab.

    If you only want to Read the files (and not Write to them) then you can use dxfuse /mnt/project.  The dxfuse is certainly available in JupyterLab, and I think it is probably available with the CLI and the Ttyd.

     

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