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help > RE: Field mapping correction for opposite phase encoded EPIs
May 19, 2022 11:05 AM | Alfonso Nieto-Castanon - Boston University
RE: Field mapping correction for opposite phase encoded EPIs
Hi Galan,
Yes, that is perfectly fine, after clicking 'Start' on that window to launch that preprocessing pipeline in the next window/prompt you will see the option where you can specify the type of fieldmap files that you are entering
Best
Alfonso
Originally posted by univ:
Yes, that is perfectly fine, after clicking 'Start' on that window to launch that preprocessing pipeline in the next window/prompt you will see the option where you can specify the type of fieldmap files that you are entering
Best
Alfonso
Originally posted by univ:
Hi Alfonso,
Thank you so much for the reply!
I followed your steps by creating a secondary dataset first. During the preprocessing stage, after selecting 'functional Creation of VDM for susceptibility distortion correction', I only saw 'Magnitude & PhaseDiff' but did not see an option of 'Pre-computed Fieldmap file (Hz)' (see the attached image). Is it okay to proceed? My CONN version is 21a.
Thank you,
Galan
Originally posted by Alfonso Nieto-Castanon:
Thank you so much for the reply!
I followed your steps by creating a secondary dataset first. During the preprocessing stage, after selecting 'functional Creation of VDM for susceptibility distortion correction', I only saw 'Magnitude & PhaseDiff' but did not see an option of 'Pre-computed Fieldmap file (Hz)' (see the attached image). Is it okay to proceed? My CONN version is 21a.
Thank you,
Galan
Originally posted by Alfonso Nieto-Castanon:
Hi
Galan,
For opposite phase encoded EPIs you need to first run FSL's topup to compute an estimated fieldmap image from the two opposite directions (e.g. --fout output from TOPUP), and then you may enter that single fieldmap file -for each subject- directly into CONN in an 'fmap' secondary dataset and proceed normally from there to preprocessing (selecting in this case in the functional_vdm_create step the option 'Pre-computed Fieldmap file (Hz)' instead of the 'Magnitude & PhaseDiff files')
Best
Alfonso
Originally posted by univ:
For opposite phase encoded EPIs you need to first run FSL's topup to compute an estimated fieldmap image from the two opposite directions (e.g. --fout output from TOPUP), and then you may enter that single fieldmap file -for each subject- directly into CONN in an 'fmap' secondary dataset and proceed normally from there to preprocessing (selecting in this case in the functional_vdm_create step the option 'Pre-computed Fieldmap file (Hz)' instead of the 'Magnitude & PhaseDiff files')
Best
Alfonso
Originally posted by univ:
Dear all,
I want to use a field map to correct for resting state fMRI data. I've checked the manual (v17) and known there is an option for importing magnitude & phase maps. I want to know if there is an option for filed mapping acquired by the opposite phase encoded EPIs sequence? If yes, how to use these files properly in CONN?
Thank you,
Galan
I want to use a field map to correct for resting state fMRI data. I've checked the manual (v17) and known there is an option for importing magnitude & phase maps. I want to know if there is an option for filed mapping acquired by the opposite phase encoded EPIs sequence? If yes, how to use these files properly in CONN?
Thank you,
Galan
Threaded View
| Title | Author | Date |
|---|---|---|
| univ | May 5, 2022 | |
| Alfonso Nieto-Castanon | May 9, 2022 | |
| univ | May 13, 2022 | |
| Alfonso Nieto-Castanon | May 19, 2022 | |
| geraldinerod | Feb 6, 2023 | |
| univ | May 20, 2022 | |