Canšt you just preprocess the data outside of FEAT (e.g. with the HCP
Pipelines or fMRIprep) and then run your analysis?
-fout should be a single volume and will be equivalent to the fieldmap if
topup was properly configured. You can use the averaged (across phase
encoding directions) distortion corrected spin echo field maps as the
magnitude image.
Matt.
On 1/29/19, 8:18 AM, "FSL - FMRIB's Software Library on behalf of Noam
Schneck" <[log in to unmask] on behalf of [log in to unmask]> wrote:
>Dear Experts,
>
>I am converting topups into fieldmaps to incorporate within a feat
>analysis of multiband EPI data. When I run the topup command as follows;
>
>topup --imain=$file/AP_PA_b0.nii.gz --datain=$file/acqparams.txt
>--config=b02b0.cnf --fout=$file/warp --iout=$file/unwarped
>
>the fout and iout results that I get each have two volumes. However, when
>I convert into fieldmap and incorporate within feat it is expecting files
>with only one volume.
>
>In each output the first volume looks like what I would expect while the
>second volume looks more like a mask. I can get around this by cutting
>out the second volume in the fout and iout results but this seems like a
>hack.
>
>Can anyone tell me why the topup procedure produces outputs with two
>volumes and what I should do with the second volumes in each file?
>
>Thanks,
>Noam
>
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