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extraction of 2D data according to non linear sampling schedule

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  • ratancbmr
    Hello, We are interested in extraction of 2D data according to non linear sampling schedule. We have a 2D data acquired in linear schedule in t1 dimension. We
    Message 1 of 5 , Feb 2, 2010
      Hello,
      We are interested in extraction of 2D data according to non linear sampling schedule. We have a 2D data acquired in linear schedule in t1 dimension. We are interested in extracting only those t1 points which are according to non linear sampling schedule. Is there any script in nmrPipe which can do the job.
      thanks
      Ratan
    • Frank Delaglio
      Greetings ... Ok, first, it might be interesting for you to note that NMRPipe has more than one method for reconstruction of Non-Uniform Sampled Data (NUS) ...
      Message 2 of 5 , Feb 2, 2010
        Greetings ...

        Ok, first, it might be interesting for you to note that NMRPipe
        has more than one method for reconstruction of Non-Uniform Sampled
        Data (NUS) ... there are examples "nusdemo2d" and "nusdemo3d" at the
        NMRPipe download site. The "README" files in these examples might
        be helpful too.

        There are many ways one could take an "ordinary" 2D FID and
        re-arrange it. In this case, I would recommend using the same
        sorting tool that we use for re-arranging NUS data to "ordinary" data ...
        the script called "nusSort.tcl".

        In this case, the script would take a "normal" NMRPipe-format FID as
        input, and also two text files. One text file would specify a list of
        integers corresponding to the complex t1 increments to keep, the first
        increment
        being "0" (zero). The other text file would simply have the parameter
        text "NDIM 2" to indicated 2D data. For example, if you wanted to
        extract complex t1 increments 0 3 4 8 16:

        nusSort.tcl -sample test.hdr -par test.par -in test.fid -out sort.fid

        The result file "sort.fid" would have a Y-axis size of 10, size it
        contains 5 complex t1 increments.

        The script will issue some warning messages, since the amount of
        data written is less that the available data in the input FID.

        --- file test.hdr:

        3
        4
        8
        16

        --- file test.par:
        NDIM 2




        Quoting ratancbmr <ratancbmr@...>:

        > Hello,
        > We are interested in extraction of 2D data according to non linear
        > sampling schedule. We have a 2D data acquired in linear schedule in
        > t1 dimension. We are interested in extracting only those t1 points
        > which are according to non linear sampling schedule. Is there any
        > script in nmrPipe which can do the job.
        > thanks
        > Ratan
        >
        >
        >
      • Ratan
        Hello, i have extractd the data as it is given here. But it does t solve my problem. we have recorded the data with uniform sampling shedule and from this i
        Message 3 of 5 , Apr 10, 2010
          Hello,
          i have extractd the data as it is given here.
          But it does't solve my problem. we have recorded the data
          with uniform sampling shedule and from this i have to extract the
          data which has Nonuniform sampling schedule(NUS). we have used the script as follows.

          nusSort.tcl -sample test.hdr -par test.par -in test.fid -out sort.fid -noexpand

          but with this schedule the extracted data does not follow the sampling schedule.suppose we have recorded the data with 256 t1
          increment and we wanted only 64 t1 point by NUS schedule then this above will provide first intial 64 t1 point. We are interested in extracting only those t1 points which are according to non linear sampling schedule.Can you tell is there any modification needed to
          do this job.

          Thanks
          Ratan



          --- In nmrpipe@yahoogroups.com, Frank Delaglio <delaglio@...> wrote:
          >
          >
          >
          > Greetings ...
          >
          > Ok, first, it might be interesting for you to note that NMRPipe
          > has more than one method for reconstruction of Non-Uniform Sampled
          > Data (NUS) ... there are examples "nusdemo2d" and "nusdemo3d" at the
          > NMRPipe download site. The "README" files in these examples might
          > be helpful too.
          >
          > There are many ways one could take an "ordinary" 2D FID and
          > re-arrange it. In this case, I would recommend using the same
          > sorting tool that we use for re-arranging NUS data to "ordinary" data ...
          > the script called "nusSort.tcl".
          >
          > In this case, the script would take a "normal" NMRPipe-format FID as
          > input, and also two text files. One text file would specify a list of
          > integers corresponding to the complex t1 increments to keep, the first
          > increment
          > being "0" (zero). The other text file would simply have the parameter
          > text "NDIM 2" to indicated 2D data. For example, if you wanted to
          > extract complex t1 increments 0 3 4 8 16:
          >
          > nusSort.tcl -sample test.hdr -par test.par -in test.fid -out sort.fid
          >
          > The result file "sort.fid" would have a Y-axis size of 10, size it
          > contains 5 complex t1 increments.
          >
          > The script will issue some warning messages, since the amount of
          > data written is less that the available data in the input FID.
          >
          > --- file test.hdr:
          >
          > 3
          > 4
          > 8
          > 16
          >
          > --- file test.par:
          > NDIM 2
          >
          >
          >
          >
          > Quoting ratancbmr <ratancbmr@...>:
          >
          > > Hello,
          > > We are interested in extraction of 2D data according to non linear
          > > sampling schedule. We have a 2D data acquired in linear schedule in
          > > t1 dimension. We are interested in extracting only those t1 points
          > > which are according to non linear sampling schedule. Is there any
          > > script in nmrPipe which can do the job.
          > > thanks
          > > Ratan
          > >
          > >
          > >
          >
        • Ratan
          Hello, I wanted to extract the data acording non Nuniform sampling schedule(NUS). I have used the nusSort.tcl to extarct the data. As for as undersatad this
          Message 4 of 5 , Apr 14, 2010
            Hello,
            I wanted to extract the data acording non Nuniform sampling schedule(NUS). I have used the nusSort.tcl to extarct the data. As for as undersatad this script is expand the data acording to given NUS schedule.if use the script like this,
            nusSort.tcl -sample test.hdr -par test.par -in test.fid -out sort.fid

            this script works good when i record the data acording to a particular schedule.

            I wanted to extract the data fron uniformly recorded data set.
            when i am using the above script then extracted data does not follow the sampling schedule. suppose I have recorded the data with 256 t1
            increment and we wanted only 64 t1 point by NUS schedule then this above will provide first intial 64 t1 point. We are interested in extracting only those t1 points which are according to non linear sampling schedule.Can you tell is there any modification needed to
            do this job.

            Thanks
            Ratan
          • xqtang2011
            Dear all£¬ I met the same condition as Ratan posted two years ago.Is there anyone have tips? Thanks in advance. tang
            Message 5 of 5 , Jun 27 6:48 PM
              Dear all£¬
              I met the same condition as Ratan posted two years ago.Is there anyone have tips?
              Thanks in advance.
              tang

              --- In nmrpipe@yahoogroups.com, "Ratan" <ratancbmr@...> wrote:
              >
              > Hello,
              > i have extractd the data as it is given here.
              > But it does't solve my problem. we have recorded the data
              > with uniform sampling shedule and from this i have to extract the
              > data which has Nonuniform sampling schedule(NUS). we have used the script as follows.
              >
              > nusSort.tcl -sample test.hdr -par test.par -in test.fid -out sort.fid -noexpand
              >
              > but with this schedule the extracted data does not follow the sampling schedule.suppose we have recorded the data with 256 t1
              > increment and we wanted only 64 t1 point by NUS schedule then this above will provide first intial 64 t1 point. We are interested in extracting only those t1 points which are according to non linear sampling schedule.Can you tell is there any modification needed to
              > do this job.
              >
              > Thanks
              > Ratan
              >
              >
              >
              > --- In nmrpipe@yahoogroups.com, Frank Delaglio <delaglio@> wrote:
              > >
              > >
              > >
              > > Greetings ...
              > >
              > > Ok, first, it might be interesting for you to note that NMRPipe
              > > has more than one method for reconstruction of Non-Uniform Sampled
              > > Data (NUS) ... there are examples "nusdemo2d" and "nusdemo3d" at the
              > > NMRPipe download site. The "README" files in these examples might
              > > be helpful too.
              > >
              > > There are many ways one could take an "ordinary" 2D FID and
              > > re-arrange it. In this case, I would recommend using the same
              > > sorting tool that we use for re-arranging NUS data to "ordinary" data ...
              > > the script called "nusSort.tcl".
              > >
              > > In this case, the script would take a "normal" NMRPipe-format FID as
              > > input, and also two text files. One text file would specify a list of
              > > integers corresponding to the complex t1 increments to keep, the first
              > > increment
              > > being "0" (zero). The other text file would simply have the parameter
              > > text "NDIM 2" to indicated 2D data. For example, if you wanted to
              > > extract complex t1 increments 0 3 4 8 16:
              > >
              > > nusSort.tcl -sample test.hdr -par test.par -in test.fid -out sort.fid
              > >
              > > The result file "sort.fid" would have a Y-axis size of 10, size it
              > > contains 5 complex t1 increments.
              > >
              > > The script will issue some warning messages, since the amount of
              > > data written is less that the available data in the input FID.
              > >
              > > --- file test.hdr:
              > >
              > > 3
              > > 4
              > > 8
              > > 16
              > >
              > > --- file test.par:
              > > NDIM 2
              > >
              > >
              > >
              > >
              > > Quoting ratancbmr <ratancbmr@>:
              > >
              > > > Hello,
              > > > We are interested in extraction of 2D data according to non linear
              > > > sampling schedule. We have a 2D data acquired in linear schedule in
              > > > t1 dimension. We are interested in extracting only those t1 points
              > > > which are according to non linear sampling schedule. Is there any
              > > > script in nmrPipe which can do the job.
              > > > thanks
              > > > Ratan
              > > >
              > > >
              > > >
              > >
              >
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