I'm working on MRS data analysis. For Siemens raw data, it is possible to open file in notepad but It's not work for GE pfile. So, how could I find header information of this type of raw data?
Thanks
Samira
Hi,
GE data is contained in two files: one is a text file and another is binary - and the latter cannot be open in a text editor. However, you can use LCModel to read it and to convert to text file.
Very best
Maria Sokol
Try using the pfile_tools python library: https://github.com/njvack/pfile-tools
>>> from pfile_tools import headers
>>> pfile = headers.Pfile.from_file('/path/to/PXXXX.7')
>>> print(pfile.revision)
20
>>> print(pfile.header.exam_number)
5313
>>> print(pfile.header.exam_datetime)
datetime(2012, 3, 6, 10, 47, 42)
Hi,
Thank you very much for your kindly response. Unfortunately, I have no access to LcModel. Also I have no idea about python. I have not been use it before.
Have you got any other suggestion ? Or I have to learn python?
Regards
Samira
GE changes its data format frequently. You need to know the version of your system. Which kind of software or computer language are you using?
Thank you for your answer,
Unfortunately, the data are not for our lab and I don't know exactly about the version of console software. I just know that the data are belong to GE optima MR 360. Also I find in .dcm image header this field that entitled as software version :
23\LX\MR softwarerelease: SV23.0_V05_1436a.
The required voxel data should be in the .shf file - it is the GE text file. Open it in Word and find the OPUSER section. Below you can find an example:
# OPUSER Fields
# -------------
# This section contains opuser values from the image header.
# Fields are:
# num_opuserfields: Number of opuser fields
# For each field line: Field_name Field_value
sagekey_opuserinfo
num_opuserfields 49
opuser0 2500
opuser1 2048
opuser2 1
opuser3 1
opuser4 64
opuser5 1
opuser6 1
opuser7 1
opuser8 20
opuser9 20
opuser10 20
opuser11 0
opuser12 0
opuser13 0
In this header fragment the opuser 8-9 are the voxel dimentions and the opuser 11-13 are the locations. In fact, GE likes to change the file formats - in such case you need some help from IT staff to write a tool for header reading :)
Dear Prof. Sokol,
Thank you very much indeed.
One more question about raw data export in GE scanners.
All data that I have got are just .7 files. We exported these file through the path of "Service Browser/Utilities/Raw File Manager. Is it true or there is another way?
Use rdgehdr function in http://rsl.stanford.edu/research/software.html
run the following code in matlab
clear;
sss = 'C:\Datalocation\';
aaa = 'dataname.7';
ccc = 'C:\(where your rdgehdr located)\';
cd (ccc);
ddd = ['rdgehdr.exe ' sss aaa];
[status,cmdout] = system(ddd);
all parameters in cmdout, display the parameter and copy or save to a text file.
Welcome
Dear Mr. Zhongxu An
I'm using MATLAB. I would like to open file "* .7". containing MRS data.
Can I ask for a hint how to retrieve raw time data from this file for further analysis? Is there an m-file that does this job?
I will be grateful for any hint.
Thank you
Zhongxu An
Dear Zhongxu An,
Unfortunately, I could not use your code and encountered the following error :
".7 does not have a recognized Genesis header... "
in cmdout. I would be very grateful if you could help me with this.
Many thanks for considering my request.
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