Hello, FSL experts,
I've been getting a WARNING when running a Fixed Effects 2nd level analysis, combining 4 runs within subject. The warning doesn't show up in the general report of the 2nd level analysis, but on the lower-level contrast log, which is generated when running the higher-level analysis.
The warning I'm getting says (full log is also pasted below):
WARNING: The passed in varcope file, var_filtered_func_data, contains voxels inside the mask with zero (or negative) values. These voxels will be excluded from the analysis.
Despite the warning, the GLM is executed normally and I get my outputs as expected - although the results seem way noisier than I would hope. As far as I can tell, the file var_filtered_func_data seems normal: values range from 0 (outside the brain) to ~14783 (>1000 in regions where I'd expect my task to modulate activity, e.g. visual cortex), although most voxels have a <1000 value. There are no negative values on the volumes.
I'm totally clueless about what can be causing this warning, so I don't even know what type of information I should add here. If you have any idea of what this message means and would like me to post an image/log, please, let me know.
Any help is greatly appreciated.
Best,
--Marcelo Mattar
Psychology PhD student
University of Pennsylvania
------------------------------------------------------------
Progress Report / Log
Started at Mon May 6 17:33:53 EDT 2013
ln -s ../.files .files
Higher-level stats
cat ../design.lcon | awk '{ print }' > design.lcon
/usr/local/fsl/bin/flameo --cope=filtered_func_data --vc=var_filtered_func_data --dvc=tdof_filtered_func_data --mask=mask --ld=stats --dm=design.mat --cs=design.grp --tc=design.con --runmode=fe
Log directory is: stats
Setting up:
ntptsing=4.000000
evs_group=1.000000
No f contrasts
WARNING: The passed in varcope file, var_filtered_func_data, contains voxels inside the mask with zero (or negative) values. These voxels will be excluded from the analysis.
nevs=1
ntpts=4
ngs=1
nvoxels=990165
Running:
nmaskvoxels=990165
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Saving results
Log directory was: stats
/bin/rm -f stats/zem* stats/zols* stats/mask* ; /bin/mv dof stats
/usr/local/fsl/bin/smoothest -d 3 -m mask -r stats/res4d > stats/smoothness
Post-stats
/usr/local/fsl/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1
echo 990165 > thresh_zstat1.vol
zstat1: DLH=0.0161906 VOLUME=990165 RESELS=313.66
/usr/local/fsl/bin/ptoz 0.05
1.644854
/usr/local/fsl/bin/fslmaths thresh_zstat1 -thr 1.644854 thresh_zstat1
/usr/local/fsl/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null
1.644866 4.716867
Rendering using zmin=1.644866 zmax=4.716867
/usr/local/fsl/bin/overlay 1 0 example_func -a thresh_zstat1 1.644866 4.716867 rendered_thresh_zstat1
/usr/local/fsl/bin/slicer rendered_thresh_zstat1 -S 2 750 rendered_thresh_zstat1.png
/bin/cp /usr/local/fsl/etc/luts/ramp.gif .ramp.gif
mkdir -p tsplot ; /usr/local/fsl/bin/tsplot . -f filtered_func_data -o tsplot
|