Dear Experts,

I am trying to modify the HCP pipeline scripts to work with macaque data (in vivo, 0.5mm isotropic). The Pipeline uses FSL and a FreeSurfer.

In FreeSurferPipeline.sh there are some steps I'm not sure how to modify them to work correctly with macaque data instead of the human data:

1- recon-all -i "$T1wImageFile"_1mm.nii.gz -subjid $SubjectID -sd $SubjectDIR -motioncor -talairach -nuintensitycor -normalization

From what I've learned so far the option -talairach works with MNI305

template. Do I need to provide a macaque equivalent template instead of the MINI305? if yes, what would be the best way to convert my macaque template to MNI305?

2- mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz "$SubjectDIR"/"$SubjectID"/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca "$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta

mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca "$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta "$SubjectDIR"/"$SubjectID"/mri/T1.mgz "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz

The two commands above use "RB_all_2008-03-26.gca" and "RB_all_withskull_2008-03-26.gca" which are freesurfer atlases for human brain. Here I have no clue how to create .gca files from my macaque images.

I appreciate any help or insight.

Thank you! Mahmoud