open-discussion > RE: Slice Timing Correction Info
Jul 25, 2013  06:07 PM | Will Foran
RE: Slice Timing Correction Info
For total clarity, after motion correcting and running pestica. Slicetime correction needs to be applied. But AFNI's 3dTshift won't do it. FSL's slicetimer will though.

Is this correct?
» 3dinfo 104_rest.moco.irfretroicor+orig.
----- HISTORY -----
[...] to3d -prefix rest.nii -time:zt 29 200 1.5sec alt+z 012-0001-00001-0.dcm 012-0002-00002-0.dcm 012-0003-00003-0.dcm ... 012-0199-00199-0.dcm 012-0200-00200-0.dcm
[...] 3dresample -orient LPI -prefix rest.nii.gz -inset rest.nii.gz
[...] 3dvolreg -prefix 104_rest.moco -base 'rest.nii.gz[0]' -dfile 104_rest_motion.txt -maxite 60 -zpad 8 rest.nii.gz
[...] 3dcopy 104_rest.moco+orig.HEAD 104_rest.moco_pestica/104_rest.moco
[...]
/Volumes/TX/subject_data/byID/104/rest/104_rest.moco_pestica
irf_retroicor(ln137)->WriteBrik(ln549)
[3dcopy and irf_retroicor history entry is from: run_pestica.sh -d 104_rest.moco  -m -b ]

» 3dTshift -overwrite -prefix 104_rest.moco.retroicor.tshift.nii.gz 104_rest.moco.irfretroicor+orig.

++ 3dTshift: AFNI version=AFNI_2011_12_21_1014 (Jul 12 2013) [64-bit]
*+ WARNING: dataset is already aligned in time!


» 3dcopy 104_rest.moco.irfretroicor+orig. 104_moco.irfret.nii.gz 
» slicetimer --odd -i 104_moco.irfret.nii.gz -o 104_moco.irfret.tshift.nii.gz  
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RE: Slice Timing Correction Info
 Will Foran Jul 25, 2013
Erik Beall Jul 30, 2013
Will Foran Jul 30, 2013