Dear FSL experts,
my name is Marta and I have contacted you recently regarding the topup.Now I would need your advice on running Eddy.
The data I am working on have been acquired with the following b-values: b0, b100 (AP),b100 (PA), b500, b1000, b1500, b2000 and b2500.
I have merged folders with b0 and b1000 in order to perform TBSS later on. As you suggested I have run the topup with b100 AP and PA.
Now, I am about to correct my data from eddy currents and I am a bit confused how to combine my merged data (b0-b1000) with my results from the topup within Eddy.
According to the FSL website I should "generate a brain mask using the corrected b0"
using fslmaths by exerting the following command: fslmaths topup_AP_PA_b0_iout -Tmean hifi_nodif
and I should call the output file hifi_nodif. In my case, I run this command with my topup_AP_PA_b100_iout. right ?
At that point I should run BET and now my question is: do I run it on my b100 results or
rather on my merged file, b0-1000 with the following command: bet hifi_nodif hifi_nodif_brain -m -f 0.2?
Which bvac and bvals I need to use:those from b100 folders or rather those of my target folder b0-1000?
Does the index file stand for a movpar file generated by the topup? Is it perhaps created with "bet hifi_nodif hifi_nodif_brain"?
I rely upon your advice in the matter.
Thank you in advance for your time and availability.
Best regrads,
Marta
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