Hello Chuck,
It sounds like the estimation of how long the flameo sub-jobs will take to complete is failing for your data. One solution is to edit
$FSLDIR/bin/feat
and change the line
if { $fmri(robust_yn) } { set howlong [ expr int( $fmri(npts) * $fmri(evs_real) / 10 ) ] }
to be more conservative
e.g.
if { $fmri(robust_yn) } { set howlong [ expr int( $fmri(npts) * $fmri(evs_real) / 5 ) ] }
will double the time estimate.
Kind Regards
Matthew
> 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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