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help > RE: Field mapping correction
Oct 15, 2020 09:10 PM | Alfonso Nieto-Castanon - Boston University
RE: Field mapping correction
Hi Madeleine,
Yes, the simplest way is perhaps to check the images named ref_*.nii and uref_*.nii which are created by CONN during the 'create_vdm' preprocessing step (those represent the "before" and "after", respectively, homogeneity correction images on a sample reference volume). You may compare them, for example, from the command line using something like:
spm_check_registration ref_FUNCTIONAL.nii uref_FUNCTIONAL.nii
(please change FUNCTIONAL above to the name of your original functional data)
Hope this helps
Alfonso
Originally posted by madeleine:
Yes, the simplest way is perhaps to check the images named ref_*.nii and uref_*.nii which are created by CONN during the 'create_vdm' preprocessing step (those represent the "before" and "after", respectively, homogeneity correction images on a sample reference volume). You may compare them, for example, from the command line using something like:
spm_check_registration ref_FUNCTIONAL.nii uref_FUNCTIONAL.nii
(please change FUNCTIONAL above to the name of your original functional data)
Hope this helps
Alfonso
Originally posted by madeleine:
Hi
Alfonso,
I have a question that is related to this thread.
I am new to rsfMRI and am using CONN 19c. I have used the pre-set pipeline for indirect normalization with fieldmaps. During the preprocessing step, I uploaded 2 mag files and 1 phase file per subject, to use for susceptibility distortion correction with field maps. I manually specified the parameters (TEs, EPI readout time, blip direction), but I'm not sure which is the correct blip direction, and have tried a direction of -1, because the phase-encoding direction of the EPI images was anterior to posterior. I want to compare the original functional scans with those after SDC-correction, side-by-side, to see if they look better/worse. Is there a way to do this in CONN? Also, which file would I need to select? The 'meanu' file?
Many thanks in advance for your help!
All the best,
Madeleine
I have a question that is related to this thread.
I am new to rsfMRI and am using CONN 19c. I have used the pre-set pipeline for indirect normalization with fieldmaps. During the preprocessing step, I uploaded 2 mag files and 1 phase file per subject, to use for susceptibility distortion correction with field maps. I manually specified the parameters (TEs, EPI readout time, blip direction), but I'm not sure which is the correct blip direction, and have tried a direction of -1, because the phase-encoding direction of the EPI images was anterior to posterior. I want to compare the original functional scans with those after SDC-correction, side-by-side, to see if they look better/worse. Is there a way to do this in CONN? Also, which file would I need to select? The 'meanu' file?
Many thanks in advance for your help!
All the best,
Madeleine
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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 | |