Loading ...
Sorry, an error occurred while loading the content.

RE: Processing interleaved pseudo 3D Bruker data

Expand Messages
  • jana
    Currently, iam trying to implement a pulse sequence which requires 10 different cpmg delays (tau) and each has two interleaved data (refocused and coupled).
    Message 1 of 4 , Jun 8, 2012
    • 0 Attachment
      Currently, iam trying to implement a pulse sequence which requires 10 different cpmg delays (tau) and each has two interleaved data (refocused and coupled). The experiment is recorded as 2D HQSC with t2= 1024 complex points (i.e total 2048) and t1=256 complex points (i.e total=512 ; Echo=256,AntiEcho=256). Echo-AntiEcho gradient is used for frequency discrimination in t1 dimension.

      The pulse program has the following looping structure

      |------------------------------
      | |-------------------------
      | | |-------------------
      | | | |---------------
      | | | | |------------
      | | | | |
      | | | | |
      | | | | |
      | | | | |
      | | | | |------------(t2 number of scans)
      | | | |----------------(interleaved refocused/coupling loop = 2 times)
      | | |--------------------(cpmg tau loop = 10 times)
      | |-------------------------(Echo/AntiEcho selection loop = 2 times)
      |-------------------------------- (t1 loop = 256 times)

      Now the problem is i have both interleaved spectra for each cpmg tau values. Considering the two interleaved spectra to be A and B, can you provide me a Nmrpipe script which can finally give me interleaved A or B separately for each tau value?

      If i can get A and B separately, i can use 'addNMR' to add or subtract subsequently.
    • delaglio@nmrscience.com
      Hi All ... Sorry I didn t write sooner. I moved from the DC area to the West Coast this week. Find me in the happy town of Campbell CA, the reputed
      Message 2 of 4 , Jun 17, 2012
      • 0 Attachment
        Hi All ...

        Sorry I didn't write sooner. I moved from the DC area to the
        West Coast this week. Find me in the happy town of Campbell CA,
        the reputed birthplace of canned Fruit Cocktail.

        As to this interesting question about interleaved data, here's
        my thinking ...

        The example below is double interleaved, and gradient-enhanced.
        The innermost loop alternates between refocused and coupled data.
        So the first step would be to seperate the original data into these
        two parts, and save each separately.

        Then, the inner loop of either one of these parts would step
        through the 10 tau values. So, the next step would be to separate
        R and C into 10 planes each, and then adjust each of these planes
        for gradient-enhancement.

        NMRPipe has a utility script called "pseudo3D.com" to help
        split an interleaved dataset into separate planes. I think this
        double interleaved data could be handled by multiple uses of
        "pseudo3D.com" ... the first use would split the data into
        two parts, then each of the two parts would be split into 10.
        It might look like this:

        Convert with "-yT 256" ... then

        pseudo3D.com -in test.fid -outDir fid -outName test%03d.dat -tau 0 1

        pseudo3D.com -in fid/test001.fid -outDir r -outName r%03d.dat -tau 0 1
        2 3 4 5 6 7 8 9 -grad

        pseudo3D.com -in fid/test002.fid -outDir c -outName c%03d.dat -tau 0 1
        2 3 4 5 6 7 8 9 -grad






        Quoting jana <jana.jk2006@...>:

        > Currently, iam trying to implement a pulse sequence which requires
        > 10 different cpmg delays (tau) and each has two interleaved data
        > (refocused and coupled). The experiment is recorded as 2D HQSC with
        > t2= 1024 complex points (i.e total 2048) and t1=256 complex points
        > (i.e total=512 ; Echo=256,AntiEcho=256). Echo-AntiEcho gradient is
        > used for frequency discrimination in t1 dimension.
        >
        > The pulse program has the following looping structure
        >
        > |------------------------------
        > | |-------------------------
        > | | |-------------------
        > | | | |---------------
        > | | | | |------------
        > | | | | |
        > | | | | |
        > | | | | |
        > | | | | |
        > | | | | |------------(t2 number of scans)
        > | | | |----------------(interleaved refocused/coupling loop = 2 times)
        > | | |--------------------(cpmg tau loop = 10 times)
        > | |-------------------------(Echo/AntiEcho selection loop = 2 times)
        > |-------------------------------- (t1 loop = 256 times)
        >
        > Now the problem is i have both interleaved spectra for each cpmg tau
        > values. Considering the two interleaved spectra to be A and B, can
        > you provide me a Nmrpipe script which can finally give me
        > interleaved A or B separately for each tau value?
        >
        > If i can get A and B separately, i can use 'addNMR' to add or
        > subtract subsequently.
        >
        >
        >
      • jana
        Dear Frank, Thanks for the clear explanation with examples on the usage of the pseudo3D.com. I will try this approach when i collect my data. Best regards,
        Message 3 of 4 , Jun 17, 2012
        • 0 Attachment
          Dear Frank,

          Thanks for the clear explanation with examples on the usage of the pseudo3D.com. I will try this approach when i collect my data.

          Best regards,
          Jana.K

          --- In nmrpipe@yahoogroups.com, delaglio@... wrote:
          >
          >
          > Hi All ...
          >
          > Sorry I didn't write sooner. I moved from the DC area to the
          > West Coast this week. Find me in the happy town of Campbell CA,
          > the reputed birthplace of canned Fruit Cocktail.
          >
          > As to this interesting question about interleaved data, here's
          > my thinking ...
          >
          > The example below is double interleaved, and gradient-enhanced.
          > The innermost loop alternates between refocused and coupled data.
          > So the first step would be to seperate the original data into these
          > two parts, and save each separately.
          >
          > Then, the inner loop of either one of these parts would step
          > through the 10 tau values. So, the next step would be to separate
          > R and C into 10 planes each, and then adjust each of these planes
          > for gradient-enhancement.
          >
          > NMRPipe has a utility script called "pseudo3D.com" to help
          > split an interleaved dataset into separate planes. I think this
          > double interleaved data could be handled by multiple uses of
          > "pseudo3D.com" ... the first use would split the data into
          > two parts, then each of the two parts would be split into 10.
          > It might look like this:
          >
          > Convert with "-yT 256" ... then
          >
          > pseudo3D.com -in test.fid -outDir fid -outName test%03d.dat -tau 0 1
          >
          > pseudo3D.com -in fid/test001.fid -outDir r -outName r%03d.dat -tau 0 1
          > 2 3 4 5 6 7 8 9 -grad
          >
          > pseudo3D.com -in fid/test002.fid -outDir c -outName c%03d.dat -tau 0 1
          > 2 3 4 5 6 7 8 9 -grad
          >
          >
          >
          >
          >
          >
          > Quoting jana <jana.jk2006@...>:
          >
          > > Currently, iam trying to implement a pulse sequence which requires
          > > 10 different cpmg delays (tau) and each has two interleaved data
          > > (refocused and coupled). The experiment is recorded as 2D HQSC with
          > > t2= 1024 complex points (i.e total 2048) and t1=256 complex points
          > > (i.e total=512 ; Echo=256,AntiEcho=256). Echo-AntiEcho gradient is
          > > used for frequency discrimination in t1 dimension.
          > >
          > > The pulse program has the following looping structure
          > >
          > > |------------------------------
          > > | |-------------------------
          > > | | |-------------------
          > > | | | |---------------
          > > | | | | |------------
          > > | | | | |
          > > | | | | |
          > > | | | | |
          > > | | | | |
          > > | | | | |------------(t2 number of scans)
          > > | | | |----------------(interleaved refocused/coupling loop = 2 times)
          > > | | |--------------------(cpmg tau loop = 10 times)
          > > | |-------------------------(Echo/AntiEcho selection loop = 2 times)
          > > |-------------------------------- (t1 loop = 256 times)
          > >
          > > Now the problem is i have both interleaved spectra for each cpmg tau
          > > values. Considering the two interleaved spectra to be A and B, can
          > > you provide me a Nmrpipe script which can finally give me
          > > interleaved A or B separately for each tau value?
          > >
          > > If i can get A and B separately, i can use 'addNMR' to add or
          > > subtract subsequently.
          > >
          > >
          > >
          >
        • jana
          Thank you Frank! I will try out your suggestion. Best regards, Jana.K
          Message 4 of 4 , Jun 17, 2012
          • 0 Attachment
            Thank you Frank!
            I will try out your suggestion.

            Best regards,
            Jana.K

            --- In nmrpipe@yahoogroups.com, delaglio@... wrote:
            >
            >
            > Hi All ...
            >
            > Sorry I didn't write sooner. I moved from the DC area to the
            > West Coast this week. Find me in the happy town of Campbell CA,
            > the reputed birthplace of canned Fruit Cocktail.
            >
            > As to this interesting question about interleaved data, here's
            > my thinking ...
            >
            > The example below is double interleaved, and gradient-enhanced.
            > The innermost loop alternates between refocused and coupled data.
            > So the first step would be to seperate the original data into these
            > two parts, and save each separately.
            >
            > Then, the inner loop of either one of these parts would step
            > through the 10 tau values. So, the next step would be to separate
            > R and C into 10 planes each, and then adjust each of these planes
            > for gradient-enhancement.
            >
            > NMRPipe has a utility script called "pseudo3D.com" to help
            > split an interleaved dataset into separate planes. I think this
            > double interleaved data could be handled by multiple uses of
            > "pseudo3D.com" ... the first use would split the data into
            > two parts, then each of the two parts would be split into 10.
            > It might look like this:
            >
            > Convert with "-yT 256" ... then
            >
            > pseudo3D.com -in test.fid -outDir fid -outName test%03d.dat -tau 0 1
            >
            > pseudo3D.com -in fid/test001.fid -outDir r -outName r%03d.dat -tau 0 1
            > 2 3 4 5 6 7 8 9 -grad
            >
            > pseudo3D.com -in fid/test002.fid -outDir c -outName c%03d.dat -tau 0 1
            > 2 3 4 5 6 7 8 9 -grad
            >
            >
            >
            >
            >
            >
            > Quoting jana <jana.jk2006@...>:
            >
            > > Currently, iam trying to implement a pulse sequence which requires
            > > 10 different cpmg delays (tau) and each has two interleaved data
            > > (refocused and coupled). The experiment is recorded as 2D HQSC with
            > > t2= 1024 complex points (i.e total 2048) and t1=256 complex points
            > > (i.e total=512 ; Echo=256,AntiEcho=256). Echo-AntiEcho gradient is
            > > used for frequency discrimination in t1 dimension.
            > >
            > > The pulse program has the following looping structure
            > >
            > > |------------------------------
            > > | |-------------------------
            > > | | |-------------------
            > > | | | |---------------
            > > | | | | |------------
            > > | | | | |
            > > | | | | |
            > > | | | | |
            > > | | | | |
            > > | | | | |------------(t2 number of scans)
            > > | | | |----------------(interleaved refocused/coupling loop = 2 times)
            > > | | |--------------------(cpmg tau loop = 10 times)
            > > | |-------------------------(Echo/AntiEcho selection loop = 2 times)
            > > |-------------------------------- (t1 loop = 256 times)
            > >
            > > Now the problem is i have both interleaved spectra for each cpmg tau
            > > values. Considering the two interleaved spectra to be A and B, can
            > > you provide me a Nmrpipe script which can finally give me
            > > interleaved A or B separately for each tau value?
            > >
            > > If i can get A and B separately, i can use 'addNMR' to add or
            > > subtract subsequently.
            > >
            > >
            > >
            >
          Your message has been successfully submitted and would be delivered to recipients shortly.