i like this post (click again to cancel)
2
i dont like this post (click again to cancel) remove favorite mark from this question (click again to restore mark)

Hi guys :

This post is related to : qa.nmrwiki.org/question/83/where-to-find-technical-information-on-varian-and-bruker-data-storage-formats......

Kirk had some good points on the forum. My question is a bit more specific , regarding the nuances of how Bruker SER files are ordered in terms of dimensions and phases, etc.....

How are the Bruker FIDs orderd ? I know that, in varian,

1- the numbers are { Real Imaginary Real Imaginary } ....... 2- the dimensions are incremented one by one, ni first, then ni2, etc..... and the procpar has information about which how the phasing is arrayed.

But Im wondering how are the equivalent ordering details in bruker obtained ? Are these in the acqu files ? I assume not..... since those describe individual dimensions. Clearly, TD and other parameters can give you some of the important meta data..... But where are the equivalents of, for example, the varian "array" parameter... which tells you about phase ordering ?

So in other words, where is the meta data about how the specific ordering of the FIDs ( in a 2D or 3D data ) SER file ?

Thanks !!!!!!!!! JAY

asked May 20 '10 at 12:34

j's gravatar image

j
131


2 Answers:
i like this answer (click again to cancel)
1
i dont like this answer (click again to cancel)

Jay,

Each individual fid is added sequentially to the ser file by the pulse sequence, and what the ordering represents is defined by the pulse sequence. There are two issues here: The detection mode in the indirect dimensions, and the ordering of the indirect dimensions for 3D and higher.

The detection mode for older data (pre-XwinNMR3) is defined by the processing parameter MC2, which will be found in the proc# file. This is an enumeration which will tell you whether the data are Magnitude, States, States-TPPI, echo-anti-echo, etc. In newer data MC2 has been replace by the acquisition parameter FnMODE, which allows the same pulse sequence to be used for different detection modes. It is similar to a combination the Varian "f1coef" parameter and the "phase" array. SpinWorks (and TopSpin) are set up to look for FnMODE first, and then use MC2 only if FnMODE is not set.

The ordering of the indirect dimensions is defined by the AQSEQ acquisition parameter, which can have the value 312 or 321 for 3D data. It is normally set automatically by the loop structure of the pulse sequence. Older data may use the AQORDER processing parameter. TopSpin is set up to look for AQSEQ first, and then use AQORDER only if AQSEQ is not defined.

This is all well described in Bruker's XwinNMR and TopSpin manuals. Also, each pulse sequence should contain documentation on the detection mode and the ordering of the dimensions. I am just starting to add 3D processing to SpinWorks, so I may be able to give you further guidance in the future.

link

answered May 21 '10 at 07:26

Kirk%20Marat's gravatar image

Kirk Marat
686

updated May 21 '10 at 07:29

I cant seem to find the file format info in the manuals. I saw on another post that there is a fileformat.pdf file which some people have access to. Kirk - do you have this file ? If so maybe you can email it to me at jayunit100 at gmail dot com ? - j (May 21 '10 at 10:06)

O.K. I'll send you a copy of this file. It doesn't say much more that has already been discussed. You have to be careful to confuse "file format" with interpretation of what those data actually mean. - Kirk Marat (May 21 '10 at 13:17)

i like this answer (click again to cancel)
0
i dont like this answer (click again to cancel)

Thanks again kirk.

The FileForm.pdf does seem to have reasonable explanations.

However it appears not to address the following to aspects :

1) The BYTEORDA parameter value in the acqus file is "1". In the manual, it sais the value should be little or big. I assume 1 corresponds to "Little".... But I wonder what value corresponds to "Big" ?

2) I noticed in some test data that there are leading zero (integers) at the beggining of each FID. I wonder what these leading zeros correspond to ? There are about 60 of them. The strings of zeros are found in the first 60 numbers of the first FID, which has a total of 2048 points. In the second fid, the 2048th through 2110th int values are all 0 as well. Thus the zeros appear to correspond to the BEGGINING of each TD FID chunk. In particular my TD values are 2048 and 128.

Im not sure what these 0s mean, but I think they might have to do with "byte block boundarys", a term mentioned but not clearly defined by the bruker documentation.

link

answered May 25 '10 at 11:41

j's gravatar image

j
131

updated May 25 '10 at 11:45

little = 0, big = 1 I'm not sure of these "zero" points at the beginning of the fid. There should be a group delay build-up time but these points are not exactly 0. Can you send me a sampe of your data (a zip file to my email would be good) - Kirk Marat (May 25 '10 at 15:42)

Your answer
Please start posting your answer anonymously - your answer will be saved within the current session and published after you log in or create a new account. Please try to give a good answer, for discussions, please use comments and please do remember to vote (login to vote)
toggle preview

powered by CNPROG