The details will depend on which brand of scanner you have, but basically you will need to modify the source code of the pulse sequence to implement CS.  The clinical vendors are starting to come out with sequences that can do CS, but the availability is still very limited. If you are using a clinical scanner and your lab has a research agreement with your vendor, you might be able to get a development version of a sequence that can do CS.  If you are using a non-clinical system, you might be able to get a pulse sequence that can do CS from another lab.

 Thanks Dr. Waggoner for your kind response. Currently I am using Bruker 7.05 T magnet with micro-imaging accessories i.e. non-clinical scanner. But we have Clinical software Bruker Paravision 6.0.1 associated with the scanner. Can you suggest me some softwares which can convert 2dseq or fid files into matlab format? What software we can utilize for removing our k-space data from high frequency region and again FT it into image? Just for checking it weather undersampled data will give us same images or not?

Both the fid file and the 2dseq files are just blocks of numbers, without any headers.  You can find details of the way the data is ordered for each file, in the Advanced Users Manual.  Because they are just blocks of numbers, you can easily read them with the matlab function fread. 

Since the fid file is the original k-space data, it would be better to work with this file.  Depending on what pulse sequence was used though, the data might need to be a significant amount of processing before it is ready for the fft.

Good Luck

Thanks Dr Waggoner for your precious time and valuable information. I will surely explore it. 

In order to implement CS in MRI sequence (especially in Bruker scanner and Paravision sofware) you need to modify not only pulse sequence but also base source code (c++) to define some new variables, etc.. for the control the undersampling scheme.

Note:

- using copyMethod script to copy which sequence you want to implement CS version on,

- do not forget to copy pulse sequence (.ppg) too.

About the 2dseq and fid files. 2dseq is images data, while fid is raw (k-space) data. Depending on what sequence was used, the order can be different. Just look on the manual like Dr. Waggoner said to understand the order (format) of the data. Then just using fread function in Matlab (R) to read whole block of data, then using reshape function to correct the orders. For example, if RARE sequence was used, the order in 2dseq canbe [NRead, Nphase1, Nphase2, NR]. where NRead, Nphase1, Nphase2 is image size in x, y, z direction, NR is number of repetitions. Moreover, you should to be carefully on the phase order too (the order of image index perhaps non-linear like 1, 2, 3, ... but it can be 1, 25, 2, 26, ....).

Good luck to you.

Thanks Dr. khieu for your suggestions.

You are welcome Dr. Rohit. If you have any further questions regarding implement CS, data format... feel free to contact to me.

Dear Dr Khieu

I need your help regarding the 2dseq file of Bruker acquired CSI data using elliptical and accumulation weighting schemes. In comparison to the Standard acquisition, the image data seems to be aligned differently in the other weighting schemes. How can I extract the data of the subspectra from this file. For instance I read a 2042x32x32 elliptical acquired 2dseq file in Matlab and I need to perform SNR calculation on every subspectra in this file. How do I know how the data is arranged. I tried finding in Bruker manuals but I couldnt get any help on this. Kindly help me with this. Many thanks. Best Regards.