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help > RE: Preprocessing and differing number of slices
Apr 22, 2014 09:04 PM | Alfonso Nieto-Castanon - Boston University
RE: Preprocessing and differing number of slices
Hi Daniel,
Could you give the attached version a try? The new version will prompt you to enter the appropriate slice order separately for each group of sessions with common number of slices (and it will process those separately). Please let me know if you run into any issues, as I have not had a chance to test this code myself yet. Also I am not totally sure whether the realignment step might also need some similar fix, since this is a somewhat rare condition (different number of slices per session, I am not asking)
Best
Alfonso
Originally posted by Daniel Fitzgerald:
Could you give the attached version a try? The new version will prompt you to enter the appropriate slice order separately for each group of sessions with common number of slices (and it will process those separately). Please let me know if you run into any issues, as I have not had a chance to test this code myself yet. Also I am not totally sure whether the realignment step might also need some similar fix, since this is a somewhat rare condition (different number of slices per session, I am not asking)
Best
Alfonso
Originally posted by Daniel Fitzgerald:
Hi Alfonso,
So that patch has been working well for us over the last year, but just today I ran into an issue where a participant having different number of slices between sessions (don't ask) kills the script. It comes up with the correct number of slices and slice-time corrects the first session but I get the following error when it tries to move on to the second:
Failed 'Slice Timing'
Improper assignment with rectangular empty matrix.
In file "/usr/local/spm8/spm_slice_timing.m" (v4310), function "spm_slice_timing" at line 232.
In file "/usr/local/spm8/config/spm_run_st.m" (v2312), function "spm_run_st" at line 25.
Running 'Realign: Estimate & Reslice'
Failed 'Realign: Estimate & Reslice'
Error using spm_bsplinc
File too small.
For this one participant I may just go ahead and reslice it manually, but would be great if we could get a similar check for between-session slice number differences.
Best wishes,
Dan
Originally posted by Alfonso Nieto-Castanon:
So that patch has been working well for us over the last year, but just today I ran into an issue where a participant having different number of slices between sessions (don't ask) kills the script. It comes up with the correct number of slices and slice-time corrects the first session but I get the following error when it tries to move on to the second:
Failed 'Slice Timing'
Improper assignment with rectangular empty matrix.
In file "/usr/local/spm8/spm_slice_timing.m" (v4310), function "spm_slice_timing" at line 232.
In file "/usr/local/spm8/config/spm_run_st.m" (v2312), function "spm_run_st" at line 25.
Running 'Realign: Estimate & Reslice'
Failed 'Realign: Estimate & Reslice'
Error using spm_bsplinc
File too small.
For this one participant I may just go ahead and reslice it manually, but would be great if we could get a similar check for between-session slice number differences.
Best wishes,
Dan
Originally posted by Alfonso Nieto-Castanon:
(...)
I believe that
should fix this issue (after this change, the wizard should prompt
you again for the slice order when the preprocessing steps
encounter a subject with different number of
acquisitions).
(...)
(...)
Threaded View
| Title | Author | Date |
|---|---|---|
| Daniel Fitzgerald | Mar 18, 2013 | |
| Alfonso Nieto-Castanon | Mar 20, 2013 | |
| Daniel Fitzgerald | Apr 22, 2014 | |
| Alfonso Nieto-Castanon | Apr 22, 2014 | |
| Daniel Fitzgerald | Apr 16, 2013 | |
| Alfonso Nieto-Castanon | May 24, 2013 | |