Dear All, I am relatively new to Freesurfer. I have just started working on TRACULA in patients with focal enhancing brain lesions.
My first question is How can I overlay contrast enhanced T1 MPRAGE with the tractography output? I tried running recon-all in both non-enhanced MPRAGE and enhanced MPRAGE (recon-all -i RawData/patientname/T1/IM-0001-0001.dcm -i RawData/patientname/T1_post/IM-0001-0001.dcm -s patientname -all), so that I could get orig file.mgz for both T1 and T1_post that I can overlay on the tractography output. However, the aparg+aseg did not come out as nice as the ones ran using only T1 precontrast. I am also wondering if I ran both T1 pre and T1 post using recon-all, which one or both of the data will be reflected in the aparg+aseg image. Is there any other way that I can obtain .mgz file from post contrast T1 MPRAGE to overlay it with the tractography output? The second question is how can I measure the distance between the enhancing lesion and tracts using freeview? Thank you very much in advance for your help, Best Regards, Supada Prakkamakul [email protected]
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