Hi all,
I'm working on a preprocessing stream that will produce data that is generally amenable to different analysis streams, including FSL. One component of this is sampling functional volumes to FreeSurfer meshes, and I want to test this component by running a simple first-level GLM with film_gls, so that I can compare the output to a volumetric GLM.
I've previously run the following volumetric analysis, which runs as expected:
film_gls --noest --fcon=run0.fts --rn=results --con=run0.con --in=mni_bold.nii.gz --pd=run0.mat --thr=0.000000
Here `mni_bold.nii.gz` is derived from a `native_bold.nii.gz`. Additionally, we sample `native_bold.nii.gz` to the subject mesh, and transform to the `fsaverage` mesh, producing `fsaverage_bold.L.func.gii`.
film_gls --noest --fcon=run0.fts --rn=results --con=run0.con --in=fsaverage_bold.L.func.gii --pd=run0.mat --thr=0.000000 --in2=smoothwm.fsaverage.L.surf.gii --mode=surface
Abbreviated output follows after the signature, but the upshot is that an exception is thrown due to a singular matrix. It's unclear to me where this issue is arising; if the design matrix were singular, it should produce an error in the volumetric analysis.
Thanks in advance for your help.
--
Chris Markiewicz
Center for Reproducible Neuroscience
Stanford University
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Standard output
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Log directory is: results
read gifti
read scalar data that is float32
... [x 180]
paradigm.getDesignMatrix().Nrows()=180
paradigm.getDesignMatrix().Ncols()=13
sizeTS=180
numTS=163842
Completed
Prewhitening and Computing PEs...
Percentage done:
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Standard error
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** DA[0] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET)
...
** DA[179] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET)
An exception has been thrown
Runtime error:- detected by Newmat: matrix is singular
MatrixType = Crout # Rows = 3; # Cols = 3
Trace: Crout(lubksb); GeneralSolvI; InvertedMatrix::Evaluate.
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