open-discussion
open-discussion > RE: Slice Timing Correction Info
Oct 8, 2013 06:10 PM | Erik Beall
RE: Slice Timing Correction Info
Hi Rocco,
the script run_pestica.sh should pick it up, as long as the timing is specified in the header file. To check, do you get this same timing information if you run:
3dAttribute TAXIS_OFFSETS
If this works, then make sure you have unset PESTICA_SLICE_TIMING prior to running run_pestica.sh on your data - to do this, you can type
unset PESTICA_SLICE_TIMING
and then run_pestica.sh script should pick it up correctly. Isaac Schwabacher figured out how to do this automatically, and I am in his debt. However, I've only tested this on my data, let me know if you get good cardiac and respiratory estimators after doing this (it should be very different and much better if it works, it should fail catastrohpically if it doesn't work and not give you anything. If you have any doubt, send me the card/resp_rawest.txt files and the pestica2_matrices_comps.mat files and I can check). apply_PESTICA2 (stage 2) uses this information, as do the RETROICOR/IRF-RETROICOR noise removal methods (stage 4-5).
Erik
Originally posted by Rocco Marchitelli:
the script run_pestica.sh should pick it up, as long as the timing is specified in the header file. To check, do you get this same timing information if you run:
3dAttribute TAXIS_OFFSETS
If this works, then make sure you have unset PESTICA_SLICE_TIMING prior to running run_pestica.sh on your data - to do this, you can type
unset PESTICA_SLICE_TIMING
and then run_pestica.sh script should pick it up correctly. Isaac Schwabacher figured out how to do this automatically, and I am in his debt. However, I've only tested this on my data, let me know if you get good cardiac and respiratory estimators after doing this (it should be very different and much better if it works, it should fail catastrohpically if it doesn't work and not give you anything. If you have any doubt, send me the card/resp_rawest.txt files and the pestica2_matrices_comps.mat files and I can check). apply_PESTICA2 (stage 2) uses this information, as do the RETROICOR/IRF-RETROICOR noise removal methods (stage 4-5).
Erik
Originally posted by Rocco Marchitelli:
Hello Erik,
Thanks for the reply on the issue regarding the coregistration between the EPI and the EPI-MNI template.
I will give you some feedback after trying the -cmass option.
I come back to slice-timing topic now because I have to apply PESTICA to EPI data from Philips scanner.
Now the problem is that I believe that NONE of the available strings in the PESTICA setup might account for Philips slice timing correction (correct me weather I am wrong).
For Philips data there is indeed a special sequence in which slices were acquired. The sequence is the following:
0 472,5 945 1417,5 1890 2295 67,5 540 1012,5 1485 1957,5 2362,5 135 607,5 1080 1552,5 2025 2430 202,5 675 1147,5 1620 2092,5 2497,5 270 742,5 1215 1687,5 2160 2565 337,5 810 1282,5 1755 2227,5 2632,5 405 877,5 1350 1822,5
Is there a way to setup PESTICA with this slice-timing configuration?
Thanks,
R.
Thanks for the reply on the issue regarding the coregistration between the EPI and the EPI-MNI template.
I will give you some feedback after trying the -cmass option.
I come back to slice-timing topic now because I have to apply PESTICA to EPI data from Philips scanner.
Now the problem is that I believe that NONE of the available strings in the PESTICA setup might account for Philips slice timing correction (correct me weather I am wrong).
For Philips data there is indeed a special sequence in which slices were acquired. The sequence is the following:
0 472,5 945 1417,5 1890 2295 67,5 540 1012,5 1485 1957,5 2362,5 135 607,5 1080 1552,5 2025 2430 202,5 675 1147,5 1620 2092,5 2497,5 270 742,5 1215 1687,5 2160 2565 337,5 810 1282,5 1755 2227,5 2632,5 405 877,5 1350 1822,5
Is there a way to setup PESTICA with this slice-timing configuration?
Thanks,
R.
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 | |