Fetal template

[Gabriela Epihova]

Hi Frank,

I am working with the fetal dHCP data: https://biomedia.github.io/dHCP-release-notes/ 

There are a few publicly available fetal atlases with a template at each gestational age available:

https://gin.g-node.org/kcl_cdb/fetal_brain_mri_atlas
http://crl.med.harvard.edu/research/fetal_brain_atlas/

I am trying to use these as a template to perform reconstruction on each individual fetal scan in dsi studio but can't create a QA and ISO files. Any suggestions of how to go about this would be very appreciated : )

Best,

Gabriela

[Frank Yeh]

I replied in another thread/email, but just reposting here in case others may find it helpful:

1. Locate the atlas folder inside the DSI Studio folder. (On macOS, right-click the app and choose "Show Package Contents" to find it.)

2. Create a new folder named human_ga28 — assuming you want to use the GA 28-week template.

3. Add your FA and MD NIfTI files to this folder, and rename them as:

   • human_ga28.QA.nii.gz for FA

   • human_ga28.ISO.nii.gz for MD

4. Place the GA28 parcellation file in the same folder. You can check the format of the label text file by referencing other atlas folders.

5. Restart DSI Studio, and load a GQI-reconstructed FIB file at Step T3 (Fiber Tracking).

6. At Step T2a, select human_ga28 and see if the normalization and atlas loading work correctly.