[Brains-users] Abbreviated Standard Workup Guide

[Hans Johnson]

Abreviated Standard Workup Tutorial

Step-by-step Procedure guide to standard work-up in BRAINS:
a  tape read onto IPL system
b  rate QA of t1, t2, (pd), image(s) using WEBRATER web page.
c  pick and save t1 resample parameters using BRAINS
d  save aligned t1 image using BRAINS or resam script
e  pick talairach parameters on ACPC aligned t1 image using BRAINS
f  pick and save t2 resample parameters using BRAINS
g  execute (pd)t2 to t1 fit using fit_mr2mr.tcsh script
gr submitted to run fit
h  visually check (pd)t2 to t1 fit using BRAINS
hb bad fit         
i  manually trace r_vb, l_vb, bg, and bw traces using BRAINS
j  segment and run neural_net for cran using auto_seg.sh script
jr submitted to run segmentation
k  quantitatively check segmentation using kappa.sh script
l  visually check segmented image using BRAINS
lb bad segmentation
m  save r_vb, l_vb, bg, and bw traces using backup script
n  trim non_cran rois using BRAINS
o  generate cran_mask.segment, visually inspect cran_mask.segment,
       determine t50 threshold using histo script, measure t50 vols,
       measure standard segmented vols all using finish.sh script.
p  save non_cran rois using backup script
q  manually trace cerebl and hemisph surface traces using BRAINS
r  generate 130 surfaces, measure surface parameters, measure zilles
       parameters using surface.s script
s  generate 190 surfaces, measure surface parameters, measure zilles
       parameters using sisod-surf.sh script
t  visually inspect 130 surfaces using BRAINS.
u  visually inspect 190 surface using BRAINS.
v  save hemisph and cerebl rois using backup script
w  data clean and post to t50 vols dataset using SAS
   data clean and post to seg vols dataset using SAS
   data clean and post to surf dataset using SAS
   data clean and post to 130 zilles dataset using SAS
x  the pdt2 original directory images can be tossed after a good fit