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help > RE: Question about the necessity of using field map to do susceptiblity distortion correction
Mar 29, 2023 01:03 AM | Alfonso Nieto-Castanon - Boston University
RE: Question about the necessity of using field map to do susceptiblity distortion correction
Hi Shuai Huang
The default volume-based pipeline (without fieldmaps) is only able to correct motion-by-susceptibility distortion interactions (coregistering all images to an "average-distortion" reference image). If you have fieldmap images, then you can use those acquisitions to estimate the difference between this "average-distortion" image and a "no-distortion" image, so in these cases (e.g. when using the 3rd pipeline in CONN) realignment will use that information to also correct the main/static susceptibility distortions (coregistering all images to a "no distortion" reference image).
And regarding how to create secondary datasets, in the Setup.Others tab, you may click on the dropdown menu (e.g. labeled 'secondary dataset...') and select there 'new dataset' or 'label datasets' to create a new dataset and to assign labels to your datasets, respectively.
Hope this helps
Alfonso
Originally posted by Shuai Huang:
The default volume-based pipeline (without fieldmaps) is only able to correct motion-by-susceptibility distortion interactions (coregistering all images to an "average-distortion" reference image). If you have fieldmap images, then you can use those acquisitions to estimate the difference between this "average-distortion" image and a "no-distortion" image, so in these cases (e.g. when using the 3rd pipeline in CONN) realignment will use that information to also correct the main/static susceptibility distortions (coregistering all images to a "no distortion" reference image).
And regarding how to create secondary datasets, in the Setup.Others tab, you may click on the dropdown menu (e.g. labeled 'secondary dataset...') and select there 'new dataset' or 'label datasets' to create a new dataset and to assign labels to your datasets, respectively.
Hope this helps
Alfonso
Originally posted by Shuai Huang:
Hello, I noticed that the following difference
between the default processing pipeline and another pipeline:
For the default preprocessing pipeline for volume-based analyses (direct normalization to MNI-space):
it shows "functional realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)"
For the 3rd preprocessing pipeline for volume-based analyses (direct normalization to MNI-space) when field maps are available:
it shows "functional realignment with susceptibility distortion correction using field maps (subject motion estimation and correction)"
It seems that they are both performing susceptibility distortion correction, but the default processing pipeline does not use the field map to do it. The tutorial said the field map was optional, and did not provide much detail on how to do it.
My questions would be:
1) Is it OK to just use the default processing pipeline?
2) How much of a difference would it make if we use the field map to do susceptibility distortion correction?
3) How do we create a secondary dataset?
There was another post that talked about "define a new secondary dataset in Setup.Functionals and name/label it 'fmap'. But I am not sure how to do it, I couldn't find any button or menu that allows me to define/create a new secondary dataset.
Thanks so much! Any help or suggestion would be appreciated.
For the default preprocessing pipeline for volume-based analyses (direct normalization to MNI-space):
it shows "functional realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)"
For the 3rd preprocessing pipeline for volume-based analyses (direct normalization to MNI-space) when field maps are available:
it shows "functional realignment with susceptibility distortion correction using field maps (subject motion estimation and correction)"
It seems that they are both performing susceptibility distortion correction, but the default processing pipeline does not use the field map to do it. The tutorial said the field map was optional, and did not provide much detail on how to do it.
My questions would be:
1) Is it OK to just use the default processing pipeline?
2) How much of a difference would it make if we use the field map to do susceptibility distortion correction?
3) How do we create a secondary dataset?
There was another post that talked about "define a new secondary dataset in Setup.Functionals and name/label it 'fmap'. But I am not sure how to do it, I couldn't find any button or menu that allows me to define/create a new secondary dataset.
Thanks so much! Any help or suggestion would be appreciated.
Threaded View
| Title | Author | Date |
|---|---|---|
| Shuai Huang | Mar 24, 2023 | |
| Alfonso Nieto-Castanon | Mar 29, 2023 | |
| Shuai Huang | Apr 4, 2023 | |
| Alfonso Nieto-Castanon | Apr 5, 2023 | |