¥Using to3d to assemble the EPI 3D+time dataset:
Hcd ../EPI_run1 ---> change directory to get at images
Hls ---> to see what files are there (should see files I.0001 . . . I.2970)
HWe do not just do to3d I.* to create a 3D+time dataset
HFor historical
reasons, the time-axis information must be given on the to3d command line.
åCannot
be modified from the GUI
HCommand line: to3d -time:zt 27 110 0 alt+z I.*
å-time:zt Þ slices
usually presented in order of space (z), then time (t)
í-time:tz is needed at some sites
íIf in
doubt, do to3d I.* or aiv I.*, use viewer to look at slices
and see their order [aiv = AFNI Image Viewer
program]
å27 110 Þ there
are 27 slices in z and 110 in t (2970 total)
å0 Þ the TR for volume
acquisition will be read from the image headers
íIf not
available, could put 2.5s or 2500 instead of this 0
åalt+z Þ slices
are gathered in alternating order in the +z direction
íMost
EPI acquisitions are really 2D multislice, spread out through time
íAFNI
header can contain information about slice timing offsets
íOther
possible modes: zero (for 3D), @filename (to specify each slice)