Recon-all for hcp data

1

Hi all,
I am preprocessing the hcp dwi data, and I want to generate the aparc+aseg.mgz file to create the connectome. When I use the command “recon-all -i T1w_acpc_dc_restore_brain.nii -s 101309 -sd . -all -noskullstrip” (the T1w_acpc_dc_restore_brain.nii has no skull), the aparc+aseg.mgz has not been generate, in fact, most of the outputs of recon-all failed to appear. My question is should I remove the -noskullstrip? But would skullstrip a brain that’s already been skull stripped be a problem in recon-all?

In addition, is it more appropriate to run this command “recon-all -i T1w_acpc_dc_restore_1.25.nii.gz -s 101309 -sd . -all” (T1w_acpc_dc_restore_1.25.nii.gz has skull)? But it seems that the neck of T1w_acpc_dc_restore_1.25.nii.gz has been removed, should add -normneck to the recon-all command?

Best wishes!
Wang

2

Hi @OWL,

There are already preprocessed FreeSurfer results and DWI publicly available for HCP data. Is there a reason you are reprocessing?

Best,
Steven

3

Thanks for your reply! I have just noticed that. I want to make sure that if the aparc+aseg.nii.gz in the T1w folder of the hcp dataset can be used to generate the connectome (desikan_killiany parcellations)using the following code:

mrconvert aparc+aseg.nii.gz aparc+aseg.mgz

labelconvert aparc+aseg.mgz /opt/freesurfer/FreeSurferColorLUT.txt
/opt/mrtrix3/share/mrtrix3/labelconvert/fs_default.txt DK.mif

tck2connectome -assignment_radial_search 2
-tck_weights_in sift_weight.txt
-out_assignment assignment.txt
tracks_10mio.tck DK.mif
connectome.csv

4

I could not tell you based on the code alone. But if you see that the parcellation looks well aligned with the streamlines then something like that should work.

5

Ok, thank you. I’m just curious if the aparc+aseg.mgz from the results of recon-all and the aparc+aseg.nii.gz from HCP mininally preprocessed pipeline are essentially the same, just in different formats.