Hi,
It sounds like you have pretty extreme artefacts in the data. I would
do all you can to identify and remove these artefacts from the "bottom
up" rather than working backwards from the higher-level analyses, if
possible. I would run MELODIC to help you characterise the artefacts,
and if your local physicist can help remove these that's great - if
not, you may be able to clean them up with MELODIC.
Cheers, Steve.
On 19 May 2009, at 16:27, Elle Parks wrote:
> 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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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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