Hi everyone,
I am currently working on the ABCD data tractography. I really appreciate the work on ABCD processing. I have two questions about ABCD data:
1.I need three freesurfer output files, mri/T1.mgz, mri/aseg.mgz, mri/aparc.a2009s+aseg.mgz. the ABCD
minimally processed T1 data have run freesurfer, so could I get these three files directly?
2.If I can’t get these three files directly, can I execute recon-all on the minimally processed T1 file, eg. sub-NDARINV0XTVAGV2_ses-baselineYear1Arm1_run-01_T1w.nii? Thanks very much.
Panshi
i dont think the freesurfer output files are available anywhere at this point in time.
If you are going to recon-all on the minimally preprocessed T1 images, you might need to skip some steps. According to their image protocol paper (Image processing and analysis methods for the Adolescent Brain Cognitive Development Study - ScienceDirect),
“Because intensity scaling and inhomogeneity correction are previously applied, the standard FreeSurfer pipeline was modified to bypass the initial intensity scaling and N3 intensity inhomogeneity correction”
Are you using mrtrix3 for the tractography?
@gerardyu Thank you! Yes, I am using mrtrix3 for the tractography.
i see. I read that the minimally preprocessed T1w images are registered to atlas space, but it doesnt seem like the minimally preprocessed dwi images are in the same atlas space?
I don’t think T1w and DWI are in the same space. So I use flirt -in T1.nii.gz -ref b0.nii.gz -out test.nii.gz -omat test.omat -dof 6 for registration.