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Dear FreeSurfer Team,
Hope you are doing well! I've run into an issue I hope you can help me with. After running recon-all on my subjects, I proceeded with the thalamic segmentation step. I'm specifically interested in extracting the mediodorsal (MD) thalamus for a subject (by first individually extracting mediodorsal lateral and mediodorsal medial nuclei and combining them using fslmaths). Before doing so, I've first converted my data from freesurfer to native space. Once I've obtained my nucleus of interest I then loaded it into DSI Studio, which I'm using to extract my tract of interest. Given the data in the DSI studio was in the native space, the MD nucleus aligned perfectly.
The problem is that DSI studio tracking takes forever when I do the registration to the native space, so instead I've decided to run a registration of my DTI data to the HCP842 template (in order to make my results comparable to some of my colleagues and to help the tracking run faster). The problem is that now when I load my dorsomedial nucleus, it doesn't appear where it should and I would need to do a different registration (my understanding is freesurfer to ICBM152 since apparently that's what HCP842 template is related to). I've been able to use the script below, but the nucleus doesn't show up quite where it should (it's showing up more anterior to the thalamus).
mri_label2vol --reg $FRESURFER_HOME/average/mni152.register.dat --seg ThalamicNuclei.v12.T1.FSvoxelSpace.mgz --temp icbm_avg_152_t1_tal_lin.nii --o ThalamicNuclei.v12.T1-anat.mgz
Any advice? Thank you in advance for your help!!