I’m using fsl_mrsi for CSI data analysis (acquired on Siemens). I’m loving the ability to visualize the data, fitted spectra etc via fsleyes. What I can’t seem to find though is a way to export values (concentrations, QC…) to a chart for further analysis/stats. It’s great I can load output files to fsleyes and click on any voxel and see the values - whether it’s segmentation or concentration - but I would like to have a “summary” chart (csv) file similar to what LCModel produces for CSI data. So once I identify voxel(s) of interest, I can use the values without having to copy/paste them from fsleyes. Feels like I’m missing something - how do people get their values for analysis?
Hi @peter ,
Glad you are liking the visualisation. My thinking was that dealing with NIfTI as outputs was more in line with other neuroimaging analysis and therefore people would be comfortable taking the numbers froward in that format, which implicitly also conveys spatial information. There’s some really nice libraries for loading/manipulating NIfTI in Python (nibabel, or fslpy), or you can use fslmaths and fslstats and the other functions to do further analysis. I’m open to creating some other outputs though.
Thanks. I’m not a friend with Python programming yet… Are there any examples anywhere how to extract spatially dependent information from nii using fslmaths / fslstats ? I’ve used those previously for image analysis, but not sure how to apply those to extract let’s say NAA value from concs/internal/NAA.nii.gz for row 7, column 8 of processed CSI dataset.