Hah, yes, that was it! I hadn't realized it required the file to be named exactly "cope1", because the GUI didn't complain when I selected COPE images with different name arrangements. Thanks.
-Benjamin Philip
On Mon, 6 Oct 2014 17:23:42 +0100, Stephen Smith <[log in to unmask]> wrote:
>Hi - most likely FEAT is just unhappy because the files are no longer following its expected naming convention (cope1.nii.gz etc)
>Cheers.
>
>
>On 6 Oct 2014, at 17:15, Benjamin Philip <[log in to unmask]> wrote:
>
>> I am trying to do a top-level (across-participants) analysis that involves doing a L/R swap on some of the participants, to match left-side-affected patients with right-side-affected patients.
>>
>> I'm pretty sure I did the swaps just fine, by taking the 2nd-level output (across runs within participant), by just flipping the output of the analysis (i.e. the COPE image): fslswapdim cope1.nii.gz -x y z flipcope1.nii.gz. The flipped image looks right in FSLview.
>>
>> However, my top-level analyses repeatedly produce this error message:
>> syntax error in expression "1 + flipcope1": variable references require preceding $
>>
>> The error happens if and only if I include a single flipped COPE file in the inputs, so the problem isn't something else in my design. The GUI thinks there's nothing wrong with the .fsf file, and a manual search of the .fsf file also reveals no mis-formatted statements.
>>
>> Can anyone help me track this error down?
>>
>> You can see my .fsf, full logfiles, and sample cope images at:
>> https://www.dropbox.com/sh/eh57xj9fa36jn27/AACKIp1QTFuM0Grzjg5AzE8ma?dl=0
>>
>> Thanks,
>>
>> -Benjamin Philip
>
>
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