Hi everyone,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I have recently started using the dt_recon processing pipeline<br>in freesurfer. I just ran a dataset through it, and had a few questions about<br>the methodology<br>1) How does the script calculate the mask from the DW data set. Is there any way <br>
to influence the mask calculation routine? I am familiar with bet/bet2 and i have<br>an set of parameters tuned to my dataset. within dt_recon, i get the entire volume<br>as a mask, while fsl generated a nice inclusive mask. Is there any way i can use<br>
the bet generated mask with dt_recon?<br>2) why is a glm fit done at the end of the processing stage? <br><br>best regards,<br>sid.<br>