Spectroscopy with lcmodel

Using lcmodel, you can analyze MR spectroscopy data.

For more information on getting set up with a Neurodesk environment, see here

Open lcmodel from the menu: Applications -> Spectroscopy -> lcmodel -> lcmodel 6.3

run

setup_lcmodel.sh

then run

lcmgui

We packed example data into the container (https://zenodo.org/record/3904443/) and we will use this to show a basic analysis.

The example data comes in the Varian fid format, so click on Varian:

and then select the fid data in: /opt/datasets/Spectra_hippocampus(rat)_TE02/s_20131015_03_BDL106_scan0/isise_01.fid

Then Change BASIS and select the appropriate basis set in /opt/datasets/Spectra_hippocampus(rat)_TE02/Control_files_Basis_set

Then hit Run LCModel:

and confirm:

then wait a couple of minutes until the analyzed spectra appear - by closing the window you can go through the results:

the results are also saved in ~/.lcmodel/saved/