help
help > RE: Realignment and Unwarp for Right-Left phase encoding
Nov 6, 2020 03:11 PM | Alfonso Nieto-Castanon - Boston University
RE: Realignment and Unwarp for Right-Left phase encoding
Hi Martin,
Yes, you are right the steps in SPM that assume data with Anterior/Posterior phase encoding direction are: a) the FieldMap toolbox field map estimation step; and b) the "realign&unwarp" procedure; but both the FieldMap toolbox fieldmap-to-vdm transformation, and the 'apply vdm' step should work just fine for any phase encoding direction.
One reasonable work-around in this case would be to create your field map or vdm files outside of CONN, and then import those vdm files into CONN's 'vdm' secondary dataset. After that, within CONN standard pipeline you may then simply remove the realign&unwarp&distortion-correction step and use instead a "functional realign (without reslicing)" step followed by a "functional susceptibility distortion correction using VDM files" step to realign and unwarp your data using those externally-created vdm files..
Hope this helps
Alfonso
Originally posted by Martin Domin:
Yes, you are right the steps in SPM that assume data with Anterior/Posterior phase encoding direction are: a) the FieldMap toolbox field map estimation step; and b) the "realign&unwarp" procedure; but both the FieldMap toolbox fieldmap-to-vdm transformation, and the 'apply vdm' step should work just fine for any phase encoding direction.
One reasonable work-around in this case would be to create your field map or vdm files outside of CONN, and then import those vdm files into CONN's 'vdm' secondary dataset. After that, within CONN standard pipeline you may then simply remove the realign&unwarp&distortion-correction step and use instead a "functional realign (without reslicing)" step followed by a "functional susceptibility distortion correction using VDM files" step to realign and unwarp your data using those externally-created vdm files..
Hope this helps
Alfonso
Originally posted by Martin Domin:
Hello!
I'm currently trying to preprocess data, that was measured in a right-to-left phase encoding direction, the field mapping and the functional series. When using the the "full" pipeline, including creation of the VDM and further use during Realign/Unwarp, CONN stops with the message, that either "j+" or "j-" phase encoding direction is expected (I'm using .json files for automatic parameter extraction). Which makes sense, as under normal circumstances the SPM Realing/Unwarp module only corrects in anterior-posterior direction, as far as I know.
Is there a way to include such data into the standard CONN preprocessing pipeline or do I have to process it outside of CONN?
Thanks in advance and best regards,
Martin
I'm currently trying to preprocess data, that was measured in a right-to-left phase encoding direction, the field mapping and the functional series. When using the the "full" pipeline, including creation of the VDM and further use during Realign/Unwarp, CONN stops with the message, that either "j+" or "j-" phase encoding direction is expected (I'm using .json files for automatic parameter extraction). Which makes sense, as under normal circumstances the SPM Realing/Unwarp module only corrects in anterior-posterior direction, as far as I know.
Is there a way to include such data into the standard CONN preprocessing pipeline or do I have to process it outside of CONN?
Thanks in advance and best regards,
Martin
Threaded View
| Title | Author | Date |
|---|---|---|
| Martin Domin | Nov 5, 2020 | |
| Alfonso Nieto-Castanon | Nov 6, 2020 | |
| Martin Domin | Nov 10, 2020 | |
| Martin Domin | Nov 12, 2020 | |
| Alfonso Nieto-Castanon | Nov 15, 2020 | |