Hi,
I am having problems with some of my images and was hoping you could help
me. I have several subjects who each received 2-4 runs pressure stimulation
while simultaneously reporting ongoing pain, which I am modeling as an EV in
the first-level analysis.
The first-level analysis runs fine, and the filtered functional data looks
normal, but when I check the varcope images a few of the subjects have lines
running through their images where the intensity is twice as high as the
neighboring voxels. And both fixed effects and Flame 1 within-subjects
averages give this error:
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=3.000000
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=3
ngs=1
nvoxels=278869
Running:
nmaskvoxels=278869
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 2 -m mask -r stats/res4d > stats/smoothness
If I then use copes from each subjects' Flame 1 average in a higher level
Flame 1 & 2 group analysis, the log reports that multiple "tmpvarcopes
contain voxels inside the mask with zero (or negative) values and will be
excluded from the analysis". Then I get a "Flame stage 2 has given an
abnormally large difference to flame stage 1" error. Furthermore, max
z-values for these voxels in the group average are five times more than they
should be.
I've gone back to the raw .hdr files and some of them have high intensity
lines outside of the brain, but I have been running BET which should remove
them. I also used fslroi to cut the image down and just see in a single
first-level run if it made a difference, but I received the same abnormal
varcopes.
I can send you a raw .hdr, filtered_func, and varcope directly if that would
be helpful - if you can advise how to fix these images I would greatly
appreciate it :)
Thanks,
Elle
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