You want to compute the field from spin echo data that is matched to your fMRI data (same matrix, FOV, slices, echo spacing). Topup does not work as well with gradient echo data because it is hard to distinguish the signal loss in fMRI data from the geometric distortion when computing the field.
Matt.
On 1/10/24, 7:54 PM, "FSL - FMRIB's Software Library on behalf of Z Sha" <[log in to unmask] <mailto:[log in to unmask]> on behalf of [log in to unmask] <mailto:[log in to unmask]>> wrote:
Hi experts,
Recently, I have been running resting-state fMRI data. I noticed that the frontal region has a distortion. So, I wanted to use "topup" function to normalize this distortion. I think topup originally is designed to normalize the distortion in dMRI data (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup>). So, if I wanted to apply "topup" function to fMRI data, it might be different. For example, before I run "topup", I need to have a file with acquisition parameters, e.g., acq_params.txt (as mentioned in the "topup" instruction). This file includes four columns:
0 1 0 0.077312
0 -1 0 0.077312
For the dMRI scan, the fourth column represents the total readout time. But, for the fMRI scan, I guess the parameter in the fourth column should be different from what is used in the dMRI data. So, I googled some docs online to check how to compute this parameter. For example, this web mentioned how to compute this parameter if one wants to apply topup to the fMRI data (https://wiki.biac.duke.edu/biac:analysis:topup_correction <https://wiki.biac.duke.edu/biac:analysis:topup_correction>). Given that you are the expert on this tool, it would be appreciated if you have any comments on how to compute this parameter in fMRI data.
I also uploaded the fMRI data with AP and PA phase encoding directions, just in case you might test it (https://drive.google.com/drive/folders/1VNnfobUCOn_y_mhC_06U5aUORP-mPdYE?usp=sharing <https://drive.google.com/drive/folders/1VNnfobUCOn_y_mhC_06U5aUORP-mPdYE?usp=sharing>).
Looking forward to your reply. Thank you so much.
Best,
Cain
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1>
This message was issued to members of http://www.jiscmail.ac.uk/FSL <http://www.jiscmail.ac.uk/FSL>, a mailing list hosted by http://www.jiscmail.ac.uk/ <http://www.jiscmail.ac.uk/>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ <https://www.jiscmail.ac.uk/policyandsecurity/>
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1
This message was issued to members of www.jiscmail.ac.uk/FSL, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
|