Hi Clark, hi Doug
fugue has an option that might help here. Here is the relevant excerpt rom
calling fugue on the command line (as in fugue of fsl 5.0.1 but I am sure this
was also present in fsl 4.1.n):
"--unwarpdir specifies direction of warping [x/y/z/x-/y-/z-] (default y)"
it seems that this might help if set correctly; Clark maybe you can hack
epidewarp.fsl to include an "export option" to supply this information to the
script?
best
Sebastian
On Nov 13, 2012, at 09:51 , Clark Fisher wrote:
> I'm using a script that calls unpacksdcmdir. Maybe there is some setting in
> our config file that forces the orientation? Nothing obvious though.
>
>
> On Nov 13, 2012, at 12:03 PM, Douglas N Greve wrote:
>
>> I'm a little confused as to why the rows are not the phase encode direction
>> to begin with. What did you use to convert the dicoms to nifti?
>> doug
>>
>> On 11/13/2012 11:59 AM, Clark Fisher wrote:
>>> Thanks Doug,
>>>
>>> Would the proper way to handle this then be to switch the rows and columns
>>> before unwarping, then switch them back before the further processing steps?
>>>
>>> -Clark
>>>
>>>
>>
>> --
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