I am working on running FSL’s PALM and am encountering an error as PALM reads the design matrix and contrast files (it seems it is successfully reading the input because it moves on from that stage despite returning some warnings about the image package “shadowing a core library function”). Here’s the command I’m running (on a Linux hpc):
./palm -i $path/zero_vs_one_betas.nii -d $path/zero_vs_one_design.csv -eb $path/zero_vs_one_grp.txt -t $path/zero_vs_one_contrast.csv -o $path/zero_vs_one -T -logp -twotail -n 5000
The shape of each file:
- zero_vs_one_betas.nii - (91, 109, 91, 20)
- zero_vs_one_design.csv - (19, 8)
- zero_vs_one_grp.txt - (19, 1)
- zero_vs_one_contrast.csv - (0, 8)
The error I’m receiving:
Reading design matrix and contrasts. error: value on right hand side of assignment is undefined error: called from: error: /fsl-palm/palm-alpha119/palm_miscread.m at line 103, column 16 error: /fsl-palm/palm-alpha119/palm_takeargs.m at line 2056, column 14 error: /fsl-palm/palm-alpha119/palm_core.m at line 33, column 11 error: /fsl-palm/palm-alpha119/palm.m at line 81, column 1
Line 103 of palm_miscread.m:
X.data = load(X.filename);
Here is what I’ve tried so far:
- I’ve re-configured all
.mexfiles as instructed in this post, as this was the first error I encountered when attempting to run palm.
- I’ve ensured that I am using Octave 3.8.2, and made sure all the necessary packages are loaded (e.g., octave’s image package, and all of the version-specific dependencies, as highlighted in this post).
- My csv files are simply 0’s and 1’s, so they meet the palm_miscread.m’s requirements that the files contain numeric values only. However, I went into nano and re-wrote all the data to ensure there were no whitespaces or csv alignment issues. Re-running palm now gives me a new error:
error: unrecognized value for sigma: LA
Otherwise, at this point I’m not sure what else to try. Any recommendations are extremely appreciated!