Spectroscopy with lcmodel
This tutorial was created by Steffen Bollmann.
Github: @stebo85 Web: mri.sbollmann.net Twitter: @sbollmann_MRI
Getting Setup with Neurodesk
For more information on getting set up with a Neurodesk environment, see hereOpen 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:
![image](https://user-images.githubusercontent.com/4021595/155111509-967055c2-7ee1-4bf5-b645-6a0b1eee3328.png)
and then select the fid data in: /opt/datasets/Spectra_hippocampus(rat)_TE02/s_20131015_03_BDL106_scan0/isise_01.fid
![image](https://user-images.githubusercontent.com/4021595/155111715-305678e9-0c60-4154-bdf3-3aa5ccfd7da1.png)
Then Change BASIS and select the appropriate basis set in /opt/datasets/Spectra_hippocampus(rat)_TE02/Control_files_Basis_set
![image](https://user-images.githubusercontent.com/4021595/155111920-9df07a57-beb1-4507-ab7e-2c260a52d91d.png)
Then hit Run LCModel:
![image](https://user-images.githubusercontent.com/4021595/155112027-11350513-7616-4158-aca7-d5c0b07397d0.png)
and confirm:
![image](https://user-images.githubusercontent.com/4021595/155112122-1b93ff25-7469-4997-8aa6-e96a6784defa.png)
then wait a couple of minutes until the analyzed spectra appear - by closing the window you can go through the results:
![image](https://user-images.githubusercontent.com/4021595/155112432-c91bbdef-4701-4fee-a37a-b3bf8f847843.png)
the results are also saved in ~/.lcmodel/saved/