Hello,
I have a study with 32 participants whose data has already passed
through first-level analysis and has been denoised. I've got 22
lower-level contrasts successfully processed for each subject. When I
try to run the higher-level analysis, it fails for about half the
participants with a mode illustrated in the output below. Essentially,
flameo fails to create a res4d.nii.gz file with the correct number of
slices, determined using nifti_tool. Note copes 18, 21 and 22 are
correct, but copes 19 and 20 are short 3 and 1 slice, respectively:
cope18
mask.nii.gz: dim 40 8 3 91 109 91 1 1 1 1
res4d.nii.gz: dim 40 8 4 91 109 91 32 1 1 1
cope19
mask.nii.gz: dim 40 8 3 91 109 91 1 1 1 1
res4d.nii.gz: dim 40 8 4 91 109 88 32 1 1 1
cope20
mask.nii.gz: dim 40 8 3 91 109 91 1 1 1 1
res4d.nii.gz: dim 40 8 4 91 109 90 32 1 1 1
cope21
mask.nii.gz: dim 40 8 3 91 109 91 1 1 1 1
res4d.nii.gz: dim 40 8 4 91 109 91 32 1 1 1
cope22
mask.nii.gz: dim 40 8 3 91 109 91 1 1 1 1
res4d.nii.gz: dim 40 8 4 91 109 91 32 1 1 1
Below is an excerpt from the report_log file showing a typical failure
("87Log directory is: stats0054") followed by a successful processing.
Finally, the FATAL ERROR results from a bad res4d file. The same
behavior occurs when using a runmode of flame1.
Processing is done on a small cluster of Core i7 machines with 3 GB RAM
per core, submitted through SGE.
I would appreciate any help in tracking down this failure and seeing the
processing through to the end. FYI, reportedly, if "Use automatic
outlier de-weighting" is unchecked (set fmri(robust_yn) 0), then
processing finishes without issue. I will start another run to confirm this.
/usr/share/fsl/5.0/bin/flameo --cope=tmpcope0000 --vc=tmpvarcope0000
--mask=tmpmask0000 --ld=stats0000 --dm=design.mat --cs=design.grp
--tc=design.con --io --runmode=ols
. . .
No f contrasts
nevs=3
ntpts=32
ngs=1
nvoxels=4254
Running:
nmaskvoxels=4254
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 87Log directory is: stats0054
Setting up:
ntptsing=32.000000
evs_group=1.000000
1.000000
1.000000
No f contrasts
nevs=3
ntpts=32
ngs=1
nvoxels=4175
Running:
nmaskvoxels=4175
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
nmaskvoxels=4175
Saving results
Log directory was: stats0054
Log directory is: stats0055
Setting up:
ntptsing=32.000000
. . .
/bin/mv stats0000 stats ; /bin/rm -rf stats?* tmp*
/bin/rm -f stats/zem* stats/zols* stats/mask* ; /bin/mv dof stats
/usr/share/fsl/5.0/bin/smoothest -d 29 -m mask -r stats/res4d >
stats/smoothness
Mask and Data (residuals/zstat) volumes MUST be the same size!
Post-stats
/usr/share/fsl/5.0/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1
Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
FATAL ERROR ENCOUNTERED
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
while executing
"if { [ catch {
for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr argin..."
(file "/usr/share/fsl/5.0/bin/feat" line 119)
--
Chuck Theobald
System Administrator
The Robert and Beverly Lewis Center for Neuroimaging
University of Oregon
P: 541-346-0343
F: 541-346-0345
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