open-discussion
open-discussion > RE: Slice Timing Correction Info
Jul 30, 2013 04:07 PM | Erik Beall
RE: Slice Timing Correction Info
I'm not sure whats going on, PESTICA
uses the AFNI MATLAB library to write the data, and I'm pretty sure
I implemented copying the slice timing information correctly on to
the written data BRIK. If I grep for TAXIS_OFFSETS in the
+orig.HEAD file, I see the same offsets copied through. I ran
3dTshift on data that I'd produced with run_pestica.sh in the same
way as yours, and I didn't get the error. Are you using
PESTICA_v2? The only thing I don't have in my history is
3dresample - I didn't use it in my processing, could you try
without 3dresample? Alternatively, you could call 3dTshift
with the -tpattern option, could you try that and see if it works
on your data?
Erik
Originally posted by Will Foran:
Erik
Originally posted by Will Foran:
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?
++ 3dTshift: AFNI version=AFNI_2011_12_21_1014 (Jul 12 2013) [64-bit]
*+ WARNING: dataset is already aligned in time!
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 ][...] 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)
» 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
» slicetimer --odd -i 104_moco.irfret.nii.gz -o 104_moco.irfret.tshift.nii.gz
Threaded View
| Title | Author | Date |
|---|---|---|
| Rocco Marchitelli | Feb 21, 2013 | |
| Rocco Marchitelli | Oct 7, 2013 | |
| Erik Beall | Oct 8, 2013 | |
| Rocco Marchitelli | Dec 19, 2013 | |
| Rocco Marchitelli | Dec 19, 2013 | |
| Rocco Marchitelli | Dec 19, 2013 | |
| Angela Abbott | Sep 5, 2013 | |
| Erik Beall | Sep 11, 2013 | |
| Angela Abbott | Sep 4, 2013 | |
| Angela Abbott | Aug 29, 2013 | |
| Erik Beall | Aug 30, 2013 | |
| Erik Beall | Feb 21, 2013 | |
| Rocco Marchitelli | Mar 15, 2013 | |
| Pouya Ghaemmaghami | Apr 15, 2013 | |
| Erik Beall | Apr 15, 2013 | |
| Pouya Ghaemmaghami | Apr 15, 2013 | |
| Erik Beall | Apr 15, 2013 | |
| Pouya Ghaemmaghami | Apr 15, 2013 | |
| Will Foran | Jul 25, 2013 | |
| Erik Beall | Jul 30, 2013 | |
| Will Foran | Jul 30, 2013 | |