Hi,

 

I am trying to decide how to proceed after manually updating a talairach since various ways I’ve tried the recon process give me different results.

 

Our group used Freesurfer 7.2 for processing data with the T2 and 3T flags as follows:

recon-all -subject $1 -i $2/rawT1.ORIG.nii.gz -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T -all

After visual inspection, I made adjustments to the talairach using tkregister2 and then used the code below to rerun the recon:

recon-all -subject $1 -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T  -all

When this was done, the talairach.xfm file was restored to the talairach from the original recon, while the talairach.xfm~ was still the fixed version. At no point in this entire process did the talairach (fixed or original) generate an error.

 

To avoid the overwriting of the talairach.xfm file, I tried using (separately) the -notalairach and -notal-check flags. For both, the talairach.xfm file stayed as the fixed talairach, but I got different aseg and aparc results.

 

I’d like to know more about how these to flags differ and if you have a recommendation on which process is best.  The plan is to eventually use this data in TRACULA. 

 

Thanks for your help,