Hi Carlos,
> I do have a another question though. If the method I had originally
> tried
> was correct, then why was the post-stats section of the log empty
> and why
> were there no cope directories created? I also seem to remember
> there were
> quite a few errors in the log, but I'd have to re-run it to show you
> since
> these results directories were deleted.
Apologies - to be clearer - when I said that your original method
would be equivalent, I meant in principle. In practise, feat is geared
up to do it the other way. I would encourage you stick to running the
analysis in the intended manner, I can not see any benefit in
expending effort to get this working.
>
> Running the group comparisons at the 2nd level (for a motor task),
> yielded
> cope directories, but no significant differences at Z=3.0, which I
> find
> somewhat odd given that the group results, upon visual inspection,
> appear
> significantly different. I will try at a lower Z, but I have a
> feeling the
> results will also be empty.
I suggest you take a look at the unthresholded z-stats to see at what
significance your blobs lie (found in the stats directory in the feat
directory).
Presumeably you are running the default FLAME stage 1 approach? So I
also suggest as a sanity check that you run group stats in OLS mode -
to avoid any problems in the unlikely event that there is something
going wrong with the lower-level variance information.
>
>
> The log file has many of the following lines:
>
> WARNING: The passed in varcope file, tmpvarcope0027, contains voxels
> inside
> the mask with zero (or negative) values. These voxels will be
> excluded from
> the analysis.
> nevs=2
> ntpts=20
> ngs=2
> nvoxels=4842
> Running:
> nmaskvoxels=4842
> 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=4842
>
> Is this normal?
This will probably be due to there being zero values in the varcope
data (the lower level variance). This can happen when one ( or more )
of the lower level inputs does not have data in some of the
corresponding group mask voxels. Those voxels will then get excluded
from the group analysis and so should not be anything to worry about.
You might want to just check (by comparing the group mask with the
varcope data) that this is what is happening.
Cheers, Mark.
----
Dr Mark Woolrich
EPSRC Advanced Research Fellow University Research Lecturer
Oxford University Centre for Functional MRI of the Brain (FMRIB),
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich
On 3 Feb 2009, at 15:49, Carlos Faraco wrote:
> Mark,
>
> Thank you for your reply.
>
> I do have a another question though. If the method I had originally
> tried
> was correct, then why was the post-stats section of the log empty
> and why
> were there no cope directories created? I also seem to remember
> there were
> quite a few errors in the log, but I'd have to re-run it to show you
> since
> these results directories were deleted.
>
> Running the group comparisons at the 2nd level (for a motor task),
> yielded
> cope directories, but no significant differences at Z=3.0, which I
> find
> somewhat odd given that the group results, upon visual inspection,
> appear
> significantly different. I will try at a lower Z, but I have a
> feeling the
> results will also be empty.
>
> The log file has many of the following lines:
>
> WARNING: The passed in varcope file, tmpvarcope0027, contains voxels
> inside
> the mask with zero (or negative) values. These voxels will be
> excluded from
> the analysis.
> nevs=2
> ntpts=20
> ngs=2
> nvoxels=4842
> Running:
> nmaskvoxels=4842
> 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=4842
>
> Is this normal?
>
> Thanks.
>
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