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Mouse-Imaging-Centre / RMINC

Statistics for MINC volumes: A library to integrate voxel-based statistics for MINC volumes into the R environment. Supports getting and writing of MINC volumes, running voxel-wise linear models, correlations, etc.; correcting for multiple comparisons using the False Discovery Rate, and more. With contributions from Jason Lerch, Chris Hammill, Jim Nikelski and Matthijs van Eede. Some additional information can be found here:
https://mouse-imaging-centre.github.io/RMINC
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RMINC/1.5.2.1 hanatLmer fails to run #244

Closed gdevenyi closed 5 years ago

gdevenyi commented 5 years ago

Checked over all the volumes and tried an hanatLm run, that works fine, error:

model = hanatLmer(~ sex + (1|mouse_id), filtered.volumes, vols)
Error in mkRespMod(fr, REML = REMLpass) : NA/NaN/Inf in 'y'
cfhammill commented 5 years ago

Want to send me an rda/rds file for this and I can have a look?

gdevenyi commented 5 years ago

RDS files attached. Renammed vols to myvols because there's also a column in filtered.volumes called "vols". Didn't fix the problem.

files.zip

cfhammill commented 5 years ago

Some subjects are missing volumes from "lobule 8 white matter" "left paramedian lobule" and "left subependymal zone". Subjects 26 31 32 35 45 53 99 182.

Fix by setting these to zero.

gdevenyi commented 5 years ago

Cool thanks.