Nadia,

You should adjust both your processing script and your conversion script. The issue is in the indirect dimesion and is due to the aquistion mode parameter. The "-aq2d" should be fine (at this stage States and States-TPPI are equivalent), however you should modify your "-yMode" to just States. This correct the 'splitting' of your spectrum. You will also need to apply a 180 deg phase shift. For this to work though, you should put the '-auto' flag after your FT functions to allow the Fourier Transform to do the appropriate sign alternation.

You could also just put the '-alt' flag after the FT, but it's not as neat, and nmrPipe will post an error message.

For those who are interested: The major purpose of the aquisition mode variable is specify either complex and real data. It does also leave information in the header about sign alteration and whether to 'negate imaginaries' that is performed by the Fourier Transform at the processing stage. This needs the FT function to have the "-auto" flag. Of course you can just use the -alt or -neg flags to do this manually for each processing script.

There is a page long description of the paramater in the man page of bruk2Pipe which I have attached below.

AQUISITION MODE
This parameter defines the data type of the given dimen-
sion,  which  controls  how the real and imaginary parts
should be stored and processed.  The acquisition mode is
usually specified as a keyword.  While there are several
possible keywords, in most cases  it  is  sufficient  to
specify  either  "Real"  or "Complex"; other options are
described in the ACQUISITION MODES  section  below.  The
acquisition  modes  are specified by the options -xMODE,
-yMODE, -zMODE, and -aMODE.

 AQUISTION MODES
 As mentioned above, the acquisition modes are  specified  by
 the  options  -xMODE, -yMODE, -zMODE, and -aMODE.  The major
 purpose of the MODE parameter is to define  whether  vectors
 from  a  given  dimension  will  be  treated as type Complex
 (separated vectors of real and imaginary data) or type  Real
 (individual   vectors   of  all-real  or  interleaved  real-
 imaginary points).  This also  defines  whether  a  real  or
 complex  Fourier  transform will be required.  Most spectral
 data dimensions will be treated as type Complex;  exceptions
 are  TPPI data, and Bruker directly-detected sequential data
 (Bruker mode QSEQ).

 As a convenience, the MODE parameter can  also  be  used  to
 define the sign adjustment or other special processing (e.g.
 for digital detection) needed for conversion and transforma-
 tion  of  the  data.   Two kinds of sign adjustment are sup-
 ported: sign alternation, and negation  of  imaginary  data.
 Sign alternation of a complex FID has the effect of exchang-
 ing the left and right halves of the corresponding spectrum,
 whereas  negation  of  imaginaries  in a complex FID has the
 effect of reversing the corresponding spectrum.

 The steps of sign adjustment  and  transformation  are  per-
 formed by the nmrPipe Fourier transform function FT.  The FT
 function will issue warning messages if the transform  being
 performed  does  not  seem  consistent  with  the parameters
 defined during conversion.  If the FT function  is  used  in
 auto  mode (via argument -auto) it will automatically select
 a transform type and sign adjustment mode based  on  conver-
 sion parameters.

 As mentioned previously, the data type (Complex or Real,  as
 given  in  the second column below) determines the relation-
 ship between the "actual size" parameters  -xN,  -yN...  and
 the  corresponding  "valid  time-domain size" parameters -xT
 -yT...  The -xN... parameters are always  specified  as  the
 total  number  of  points (real + imaginary) recorded in the
 input file.  For type complex data,  the  -xT...  parameters
 are  specified  in complex points, so these values will usu-
 ally be half of the corresponding  -xN...  values.   In  the
 case  of type real data, the -xT... parameters are specified
 as total points, so that the corresponding values for -xN...
 and -xT... will usually be the same.

 Two special but equivalent MODE  keywords,  "Rance-Kay"  and
 "Echo-AntiEcho",  are  provided for shuffling and conversion
 of gradient-enhanced dimensions.  If one of  these  keywords
 is  used,  the  data  will  be automatically sent through an
 appropriate shuffling macro during conversion,  without  the
 need  for  any  other  special adjustments to the conversion
 command.

 Possible keywords for the MODE parameter are  listed  below;
 note that the keywords are not case-sensitive, and some key-
 words are equivalent to others.  Note the  special  keywords
 for   Bruker  data:  "Sequential"  (or  "Bruker")  for  data
 detected in Bruker's QSEQ mode, and "DQD" for digital  over-
 sampled  complex  data  detected  in  Bruker's  Digital Quad
 Detection mode:

        oooooooooooo   oooooooo ooooooooooo ooooooooooooooo
        ACQ MODE       DATA AND NEEDS SIGN  NEEDS NEGATION
        KEYWORD        FT TYPE  ALTERNATION OF IMAGINARIES
        oooooooooooo   oooooooo ooooooooooo ooooooooooooooo

        Complex        Complex  No          No
        States         Complex  No          No
        States-TPPI    Complex  Yes         No
        DQD            Complex  No          No

        Complex-N      Complex  No          Yes
        States-N       Complex  No          Yes
        States-TPPI-N  Complex  Yes         Yes

        Rance-Kay      Complex  Sometimes   Sometimes
        Echo-AntiEcho  Complex  Sometimes   Sometimes

        Real           Real     No          No
        TPPI           Real     No          No
        Sequential     Real     Yes         No
        Bruker         Real     Yes         No
        oooooooooooo   oooooooo ooooooooooo ooooooooooooooo

Hope that helps.

I can advise you to put in the fid.com file for -yMODE "complex" and in nmrpipe processing file, put | nmrPipe -fn FT -alt \

hope that can help you...