help
help > RE: Field mapping correction
Feb 15, 2019 08:02 PM | Alfonso Nieto-Castanon - Boston University
RE: Field mapping correction
Hi Victoria,
Regarding the format of fieldmap files supported by CONN's vdm_create procedure, the list of supported formats is generally available in the conn_batch help (look for "vdm_type") and it also appears in the gui after selecting this preprocessing step in the menu named "fieldmap type". Currently we support:
1) one magnitude image and one phase difference image
2) two magnitude images and one phase difference image
3) four images containing the real and imaginary parts of the short and long echo acquisitions
and 4) a single image containing a pre-calculated and unwrapped fieldmap map (typically in Hz units, but also supported rad/s or tesla units as long as the correct units are specified in the 'Units' field of an accompanying json file)
When using phase difference images these are automatically scaled and unwrapped by SPM algorithm (so they can be in any arbitrary units and they do not need to be previously unwrapped)
I believe these are some of the most common formats/scenarios, but please do let me know if you run into other scenarios as I will be happy to add other variants here to try to make this procedure as helpful and general as possible
Best
Alfonso
Originally posted by Victoria Okuneye:
Regarding the format of fieldmap files supported by CONN's vdm_create procedure, the list of supported formats is generally available in the conn_batch help (look for "vdm_type") and it also appears in the gui after selecting this preprocessing step in the menu named "fieldmap type". Currently we support:
1) one magnitude image and one phase difference image
2) two magnitude images and one phase difference image
3) four images containing the real and imaginary parts of the short and long echo acquisitions
and 4) a single image containing a pre-calculated and unwrapped fieldmap map (typically in Hz units, but also supported rad/s or tesla units as long as the correct units are specified in the 'Units' field of an accompanying json file)
When using phase difference images these are automatically scaled and unwrapped by SPM algorithm (so they can be in any arbitrary units and they do not need to be previously unwrapped)
I believe these are some of the most common formats/scenarios, but please do let me know if you run into other scenarios as I will be happy to add other variants here to try to make this procedure as helpful and general as possible
Best
Alfonso
Originally posted by Victoria Okuneye:
Hi Alfonso,
I'm also interested in using the CONN fieldmap feature.
Can you further clarify the format the fieldmap images need to be in to work with CONN create vdm feature?
I'm asking because the fieldmaps come in many different forms from the scanners and I want to make sure I'm uploading the correct form.
I know you said Phase and Magnitude - Is 2 images only or can it be the short and long echo pair for Phase and Magnitude?
Also does it have to be in wrappped or unwrapped form, is there a specific range of values needed for the maps?
Best,
Victoria Okuneye
I'm also interested in using the CONN fieldmap feature.
Can you further clarify the format the fieldmap images need to be in to work with CONN create vdm feature?
I'm asking because the fieldmaps come in many different forms from the scanners and I want to make sure I'm uploading the correct form.
I know you said Phase and Magnitude - Is 2 images only or can it be the short and long echo pair for Phase and Magnitude?
Also does it have to be in wrappped or unwrapped form, is there a specific range of values needed for the maps?
Best,
Victoria Okuneye
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| Title | Author | Date |
|---|---|---|
| Dayana Hayek | Feb 13, 2019 | |
| jothini | Mar 1, 2024 | |
| Yi Ding | Nov 20, 2020 | |
| Dayana Hayek | Mar 6, 2019 | |
| boris | Feb 22, 2019 | |
| Alfonso Nieto-Castanon | Feb 27, 2019 | |
| boris | Feb 27, 2019 | |
| Zhaoxia Qin | Feb 22, 2019 | |
| Alfonso Nieto-Castanon | Feb 14, 2019 | |
| Dayana Hayek | Feb 15, 2019 | |
| Alfonso Nieto-Castanon | Feb 15, 2019 | |
| Juan Dominguez | Feb 27, 2019 | |
| Alfonso Nieto-Castanon | Feb 27, 2019 | |
| Dayana Hayek | Feb 20, 2019 | |
| Alfonso Nieto-Castanon | Feb 20, 2019 | |
| Dayana Hayek | Feb 20, 2019 | |
| Victoria Okuneye | Feb 15, 2019 | |
| Alfonso Nieto-Castanon | Feb 15, 2019 | |
| madeleine | Oct 15, 2020 | |
| Alfonso Nieto-Castanon | Oct 15, 2020 | |
| madeleine | Oct 16, 2020 | |
| madeleine | Oct 19, 2020 | |