Hi FreeSurfer experts!

I am kind of new to FreeSurfer and this is my first time using the software!

I am using Freesurfer to create a corrtical mask for M1 for probabilistic Tracking in FSL.
I am doing recon-all for segmentation, then in tksurfer I am selecting a label for the precentral gyrus for the left hemisphere for the subject of interest. The label is selected in the same subject in which I am planning on doing the mask, so I think it is not necessary to do label2label.
Afterwards, I am doing vol2roi which gives me a .nii output. When plotting this in FSL, I have a complete misalignment of the ROI, which is not corrected by swapping the image.
Obviously this means I am having problems with the registration. How can I improve this? I have been using the mni152register.dat for the registration, and I also tried doing fslregister before running vol2roi.
I have also tried using label2vol but the output has given me the same problem.
Which of the tools is better for this type of process label2vol or vol2roi?
I attached a snapshot of the way the mask looks, (which is really bad)

Am I following an adequate procedure, does this make any sense at all, is this a good approach to integrating FreeSurfer with FSL? Is there a more efficient way to do cortical masks?

I would really appreciate any help!

Thank you
 
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Natalia Sanchez