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help > RE: Potential bugs in preprocessing pipeline
Sep 25, 2018 02:09 PM | Alfonso Nieto-Castanon - Boston University
RE: Potential bugs in preprocessing pipeline
Dear Pravesh,
As always thanks for your comments and feedback. The rationale for selecting the mid-time slice as reference when performing slice-timing correction in CONN is in order to attempt to minimize the average temporal displacement that needs to be corrected across all slices (each slice is corrected -i.e. time-shifted- by an amount equal to its actual acquisition time minus the acquisition time of the reference slice). In any way, perhaps I am missing something here so please feel free to clarify why you believe in this case selecting the mid-slice as reference could be more appropriate or preferable.
Also, regarding your previous message, sorry the patch I sent you had too many dependencies with other version-18b changes. If you do not mind, please feel free to download the code in https://www.conn-toolbox.org/resources/s... to get the current development version -that already includes the patch that I sent you- (the final 18b version should be released in the next few weeks and that will become available as always here at nitrc.org)
Thanks
Alfonso
Originally posted by Pravesh Parekh:
As always thanks for your comments and feedback. The rationale for selecting the mid-time slice as reference when performing slice-timing correction in CONN is in order to attempt to minimize the average temporal displacement that needs to be corrected across all slices (each slice is corrected -i.e. time-shifted- by an amount equal to its actual acquisition time minus the acquisition time of the reference slice). In any way, perhaps I am missing something here so please feel free to clarify why you believe in this case selecting the mid-slice as reference could be more appropriate or preferable.
Also, regarding your previous message, sorry the patch I sent you had too many dependencies with other version-18b changes. If you do not mind, please feel free to download the code in https://www.conn-toolbox.org/resources/s... to get the current development version -that already includes the patch that I sent you- (the final 18b version should be released in the next few weeks and that will become available as always here at nitrc.org)
Thanks
Alfonso
Originally posted by Pravesh Parekh:
Dear Dr. Alfonso,
I think there may be another bug in the pre-processing pipeline. When performing slice timing correction and selecting BIDS to pick up slicing order (actually timing), the reference slice is specified as half the last slice time i.e. say the last slice was acquired at 2250ms, then the reference slice is specified as 1125ms. I am assuming that instead of this, the timing for the middle slice is what needs to be picked up.
Regards
Pravesh
I think there may be another bug in the pre-processing pipeline. When performing slice timing correction and selecting BIDS to pick up slicing order (actually timing), the reference slice is specified as half the last slice time i.e. say the last slice was acquired at 2250ms, then the reference slice is specified as 1125ms. I am assuming that instead of this, the timing for the middle slice is what needs to be picked up.
Regards
Pravesh
Threaded View
| Title | Author | Date |
|---|---|---|
| Pravesh Parekh | Sep 1, 2018 | |
| Pravesh Parekh | Oct 10, 2018 | |
| Pravesh Parekh | Oct 4, 2018 | |
| Pravesh Parekh | Sep 17, 2018 | |
| Alfonso Nieto-Castanon | Sep 25, 2018 | |
| Pravesh Parekh | Sep 26, 2018 | |
| Alfonso Nieto-Castanon | Oct 10, 2018 | |
| Pravesh Parekh | Oct 11, 2018 | |
| Alfonso Nieto-Castanon | Oct 12, 2018 | |
| Pravesh Parekh | Dec 6, 2018 | |
| Alfonso Nieto-Castanon | Dec 9, 2018 | |
| Jeff Browndyke | Dec 10, 2018 | |
| Pravesh Parekh | Dec 11, 2018 | |
| Pravesh Parekh | Sep 25, 2018 | |
| Pravesh Parekh | Sep 12, 2018 | |
| Alfonso Nieto-Castanon | Sep 3, 2018 | |
| Pravesh Parekh | Sep 5, 2018 | |