fsfast does not work with topup in this way. You can do a couple of
things (1) do the preprocessing yourself and then turn it off for fsfast
(2) create your own B0 map and put it in to sessid/fsd/b0dcmap.nii.gz
and specify -b0dc in mkanalysis-sess
On 12/8/2022 9:50 AM, Asa Borzabadi Farahani wrote:
External Email - Use Caution
Hi,
I have two basic questions.
1- I am currently having some AP fMRI runs and I have also acquired a
single PA run to be able to do distortion correction, my original plan
was to use FSL and apply topup to get the undistorted fMRI data. How
can I fit it within the preproc-sess command? ( I suppose the motion
correction and slice timing correction should be done before topup),
could you please suggest me what is more appropriate to do?
2- In my study, for each subject I did 8 runs in a single data
acquisition session. The runs that I have are 2 different types; The
first type of runs ( 4 runs) have black background and the other 4
runs have the gray background. My ultimate goal is to compare these 2
conditions in a group and subject level. Do you suggest that in the
functional folder, I create two sessions per subject and put the four
runs with gray background in session 1 and the other four runs with
the black background in session 2?
Thank you so much for your time and consideration.
Asa Farahani
Sent from Mail
<https://secure-web.cisco.com/14-OsICoCS2xDYjCLpXfqNBQLlPmq6KfR6gvoFX6GyqCqlaPr8PxhOk_8UiLLOvuCnvImp_9wWSbODZwZiOj00zNRyCuaK-p2msVqLhnpxBzw06IbI4y5tVCoBp4WACY8yg3hEjAkQ0PRKiA_Nlto72jaewISn5VafPxpAUObjg1y9D2VkkFssqZoTovDa72v3-fi2Msn0ApDAZ0wQ7yf7YhY7zpMyN36pbreW3jRHY2uoPs8StuqcOTqyZKyYJW7MuYuJ1N1B6sovVYhLTLlzyDQD95FyAgD8iJ_6cSJP9AadmLF68t7etk_08n3KDLy/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986>
for Windows
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
