Dear Bruce, Dear Anastasia,
I would like to investigate white matter changes in a group of elderly patients. The acquired DWI data are 6-gradient-direction+1-non-DWI images by a clinic routine (not by me unfortunately). The meaningful analyses may be ROI-based DTI model considering FA, MD etc. measures to perform group comparisons. Subcortical ROIs like thalamus, putamen in aseg as well as white matter bundles like *h.cst_AS etc. in TRACULA are of my research interests. I would like to kindly ask the following questions:
1. To compute FA/MD of thalamus for instance, shall I simply apply individual thalamus mask extracted from aseg to wmparc then output the results in .stats files?
2. TRACULA analysis works with my DWI data (6 gradient-direction) so I could extract masks of the 18 tracts, which serve as ROIs in the FA/MD group analysis. I wonder whether there exists a better alternative to extract fiber bundle masks? The practical issue is that it takes >20 hours to process single patient and I have hundreds and it's accumulating.
3. Is there a new development to enable adding new labels to the TRACULA atlas? I would like to include Corona Radiata, Inferior Fronto-Occipital Fasciculus, Olfactory Tract etc. So far I only found this post to do it manually: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31955.html.
Thank you all very much in advance!
Kind regards,
Yong