Myelin map data is missing for many subjects when downloaded through the dhcp_3rd_anat_pipeline torrent

Hi,

I downloaded dHCP data through the dhcp_3rd_anat_pipeline torrent.
I noticed that myelin map data is missing for many subjects, for instance:

  • sub-CC00227XX13\ses-92100
  • sub-CC00084XX11\ses-31201
  • sub-CC00371XX09\ses-134700
  • sub-CC00319XX14\ses-117300
  • sub-CC00217XX11\ses-73700
  • sub-CC00143AN12\ses-47501
  • sub-CC00468XX15\ses-139100
  • sub-CC00061XX04\ses-13300
  • sub-CC00170XX06\ses-56100
  • sub-CC00341XX12\ses-108000
  • sub-CC00501XX06\ses-146500
  • sub-CC00291XX12\ses-93100
  • sub-CC00307XX10\ses-98800
  • sub-CC00221XX07\ses-75000
    Could you make this data accessible somehow?
    (I don’t want to install and run the whole pipeline.)

Hi,

Do these subjects have a usable T1?

Logan

No, the ‘anat/sub-{subid}_ses-{sesid}_rec-SVR_T1w.nii’ files are not present in the raw dataset.

But then my question is, how did you derive the myelin map of these subjects in some of your follow-up works? Here, for instance, these subjects are included in the training set.

Hi,

The list of subjects used for the benchmarking, and subsequent analyses using surface transformers, was derived prior to the official 3rd release of the dHCP (@EmmaR and I ran cortical surface processing and registration etc). If you want access to the list of data that we used for this task, I can grant you access to the data repo if you send me an email (logan.williams [at] kcl.ac.uk with 1) screenshot confirming you have access to the third release dHCP dataset and 2) an account name for https://gin.g-node.org/. These are the same terms as the SLCN challenge (Data Access - Grand Challenge).

Logan

Thank you!
I already have access to this dataset, but I’d like to work with the raw mesh data, where each vertex has associated features.

Oh okay - in that case, you can resample the metrics to the native space/template surfaces using wb_command -metric-resample (Connectome - Workbench Commands).

Logan

Thank you again for the quick help!
I guess I’ll just disregard those subjects whose T1/myelinmap is not available in the official release.