Just to add to this:
any -- option needs an equals sign '=' after it.
So the full line that you would need is:
fugue -i epi -p unwrapped_phase -d 0.295 -u unwarped_epi --savefmap=epishifttest
All the best,
Mark
Christopher Bailey wrote:
>Hi,
>
>Try adding a dash (-) before -savefmap; it should be --savefmap
>
>fugue -i epi -p unwrapped_phase -d 0.295 -u unwarped_epi --savefmap
>epishifttest
>
>The same for --saveshift (two dashes followed by the filename).
>
>-Chris
>
>On Tue, 2005-01-04 at 11:31 +0000, R Huang wrote:
>
>
>>Hello
>>
>>
>>I have a problem about how to run command lines.
>>
>>I wanted to use the command 'fugue' to save pixel shift volume (just for
>>learning) and tried
>> 'fugue -i epi -p unwrapped_phase -d 0.295 -u unwarped_epi -savefmap
>>epishifttest'
>>and other combinations. Then the following messages come out
>>
>>... ...
>>Optional arguments (You may optionally specify one or more of):
>> -i,--in filename of input volume
>> -u,--unwarp apply unwarping and save as filename
>> -w,--warp apply forward warp and save as filename
>> -p,--phasemap filename for input phase image
>> -d,--dwelltoasym set the dwell to asym time ratio
>> --dwell set the EPI dwell time per phase-encode line (sec)
>> --asym set the fieldmap asymmetric spin echo time (sec)
>> --savefmap filename for saving fieldmap (rad/s)
>> --loadfmap filename for loading fieldmap (rad/s)
>> --saveshift filename for saving pixel shift volume
>> --loadshift filename for reading pixel shift volume
>>... ...
>>There were errors parsing the command line!
>>
>>
>>Could you please point out how to use
>> '-i,--in filename of input volume
>> ... ...
>> --saveshift filename for saving pixel shift volume'?
>>
>>Of course, if have some examples will be very great.
>>
>>
>>Thanks in advance
>>
>>rhuang
>>
>>
>--
>
>
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