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Hi Ronald,
for now a quick remedy for the first problem:
in case there is any period in a filename add the additional period in the end of the filename
i.e.
XXXXX_NoWSTR3500TE24.5_16ave.
instead of
XXXXX_NoWSTR3500TE24.5_16ave<<<< After a save-as the filename in the spectrum display window header is not updated. Does this mean the next Ctrl-S save is still under the original filename? No, Ctrl-S will save the updated data under the new filename. Only the name in the window is not updated (we will fix this) <<<
Try to open the loading dialogue using “File”|”Open as…”
In the list box choose “Bruker SER Format”. Then select multiple folders containing the FID files.
JanaDear Laurie,
What files do you load (fid, ser, rawdata.job0)? Do you load multiple files? Or are your series store in one file?
JanaDear Samuel,
How did you convert the jMRUI basis set to the LCmodel format? Obviously, your LCmodel basis set is complex conjugated. To fix it, conjugate the basis set.
Jana
Make sure that a signal representing noise has the same number of points, same sampling interval and the same transmitter frequency as signals in your basis set.
To change the sampling interval and the transmitter frequency of the simulated noise load the simulated noise into the 1D mode. In the 1D mode menu select menu item File | Signal Information and enter the desired transmitter frequency and the sampling interval (the same as is in your basis set).
Hint for version 5.2 and higher: From NMRScopeB you can save simulated metabolites directly into a metabolites list (.ml file) and thus you do not have to create a basis set (metabolites list) from individual metabolites in QUEST (instead you can directly load your simulated .ml file as a basis set).
Metabolites list (.ml file) can be also loaded into 1D mode where you can see and manipulate all simulated metabolites (e.g. to sum them etc.).Jana
We found out that the troubled data were not spectra but 1d spatial data (they were acquired with a gradient ON). From this reason they cannot be loaded to jMRUI.
For simulation of a basis set you have to use the same pulse sequence and acquisition parameters as you used in your experiment.
Please would you send me your data (zipped folder) and your NMRSCOPE-B setup (in a NMRSCOPE-B window in “File” choose “Save Experiment & Physics”). Then zip the folder in which you stored the NMRSCOPE-B setup.
You will find my email at http://www.jmrui.eu/about/coordinator-developers/What do you mean by the example data sets ?
We distribute the example data sets only for SpectrIm and those data can be downloaded from http://www.jmrui.eu/license-and-download/download-beta-release/
They are not included in the installation package.Jana
Have you ever opened your data with jMRUI successfully in past (i.e. fid was identified as fid)?
If not please would you provide me with the troubled data by sending the zipped folder to ?
If you successfully opened the data in past however, removal of the jmrui.ini file should help ( jMRUI will behave as you were started it for the first time and will create a new default jmrui.ini file).There was a bug in the version 5.2 that has been removed in the version 6.0. To remedy the problem in version 5.2 please remove the Mrui.init file from the .emrui sub-directory in your users home directory (https://en.wikipedia.org/wiki/Home_directory).
Note: the bug is not related to the Bruker data format
Jana
After you load the acquired spectra, you should calibrate the frequency axis. To do so, right click a peak of your choice in the spectrum, select “Set reference” and enter the corresponding reference frequency numerically in the dialog box.
Then in QUEST the spectra and the basis set simulated with NMRScope-B should be aligned.Jana
You should load fid.
If you have problems with loading your data the most probably you do not have jmrui correctly installed. Please, first check if you have 32-bit java installed on your computer (you should have java.exe file in C:\Program Files (x86)\Java\\bin directory, where is the name of the java version you have installed. If you do not have 32-bit java installed, please install it.
Then modify jmrui.bat and jmrucl.bat files as described in the readme.txt i.e. you should have full path of your java.exe specified on the first row in batch files (without extension exe):set javaFile=”C:\Program Files (x86)\Java\
\bin\java” Please let us know if the above solved your problem
With best regards
Jana
