Hello,
I have a CSV file that includes numerous specimens, each with multiple landmark coordinates. Additionally, there are several FRM files for each specimen, also containing various landmark coordinates.
Is there a method to upload this CSV file to generate GPA and PCA? Alternatively, is there a way to convert these different files into the FCSV or JSON format for further analysis?
Thank you,
Ariana
There is nothing in Slicer that will convert this CSV format in a way that Slicer expects the coordinate data.
With a little scripting you can convert that into FCSV format, which expects each landmarks to be a row of data matrix (see the format here: Markups — 3D Slicer documentation)
If you are comfortable with R, read this csv file into your R session, convert it into the 2D array in which each coordinate is a row, then use the SlicerMorphR extension to write the FCSV file.
you can use devtools to install SlicerMorphR
'devtools::install_github(“SlicerMorph/SlicerMorphR”)
Each of your samples (rows in your original data) should be written as a separate FCSV file. You can then use the GPA module in SlicerMorph to do the GPA alignment and PCA decomposition and visualize the results.
