Hi, I have a problem with analysing a slightly complicated design in
FEAT and would
like some advice about FEAT internals.
Main question. Is it possible *in principle* to set up a third level
model in FEAT which
takes its inputs from a mixture of 1st level COPES and 2nd level COPES?
(1) Background. I have a design that looks like this
Subject TASK Run Repeat
1 A 1
1 B 1
2 A 1
2 B 1
2 A 2
2 B 2
3 A 1
3 B 1
3 A 2
3 B 2
...
etc
In other words all subjects *except* the first subject do 2 runs of
task A and 2 runs of task B. But subject 1 did only 1 run of task A
and task B.
I have previously analysed this data set using v3.3 of FEAT and
following the instructions for
the 3 level multisubject multisession design using a 2nd level
analysis to model the cross
session variance. This worked fine. I suppose I should have stopped
when I was ahead but
alas I did not. Eager to see what surprises awaited me I then tried
reananlysing (using v3.3) the data with the new advice now given for
FSL v4 on multisubject multisession designs. I created new 2nd level
FE analyses for all subjects (*except* subject 1) using a higher level
FE design to combine the 2 runs for task A and the 2 runs for task B.
At this stage I have
Subject Task FEAT Level
1 A 1
1 B 1
2 A 2
2 B 2
3 A 2
3 B 2
..
etc
(2) Firstly, I tried to combine these at third level (e.g. simple
group average for task A) by
using as input FEAT dirs:
subject1_A.feat
subject2_A.gfeat
subject3_A.gfeat
etc
This fails with "Error - registration has not been run" for all inputs
after subject 1.
Clearly, this is a wrong thing to do.
Q: I assume at this point that I cannot use the above option of using
"lower level FEAT dirs" because there is a mismatch between the two
levels?
Subjects 2 onwards are level 2 .gfeat analyses. Inside these directories
are cope1.feat etc that relate only to EV 1, whereas the subject 1
level 1 .feat
directory contains all the stats/cope images and reg_standard/stats/cope images.
So I assume it also makes no sense to setup a 3rd level model with inputs:
subject1_A.feat
subject2_A.gfeat/cope1.feat
subject3_A.gfeat/cope1.feat
etc?
Thus, it seems I need to use as input type "3D COPE images from FEAT dirs"
Q: I hope all my assumptions and logic are correct so far?
(3) I then set up a third level model for the simple group average for
EV1 in task A by
using as inputs the COPEs
subject1_A.feat/stats/cope1.nii.gz
subject2_A.gfeat/cope1.feat/stats/cope1.nii.gz
subject3_A.gfeat/cope1.feat/stats/cope1.nii.gz
and ran this. It *appeared* to work and produced rendered images
(but see below)
(4) Encouraged, I went on and reran my more complicated 2x3 factorial design
that I have previously emailed you about:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0707&L=FSL&P=R40723&I=-3
Although this *appeared* to run, the rendered stats images showed no
activation - completely different to the previous analysis I had run
using the earlier recipe for multisubject multisession analysis that
the FSL web page showed. Digging into the
log files showed multiple errors like this in cope1.feat/report.log:
/usr/local/fsl/bin/avwroi tdof_filtered_func_data tmptdof9 0 91 0 109 9 1
/usr/local/fsl/bin/flame --cope=tmpcope9 --vc=tmpvarcope9
--dvc=tmptdof9 --mask=tmpmask9 --ld=stats9 --dm=design.mat
--cs=design.grp --tc=design.con --fc=design.fts --ols --nj=10000
--bi=500 --se=1 --fm
--zlt=2.25 --zut=2.65
Log directory is: stats9
Setting up:
nevs=21
ntpts=96
ngs=1
nvoxels=88
Running:
nmaskvoxels=2
njumps = 10000
burnin = 500
sampleevery = 1
nsamples = 9500
Metropolis Hasting Sampling
Number of voxels=2
Percentage done:
1
An exception has been thrown
Logic error:- detected by Newmat: index error: requested index = 91
MatrixType = Rect # Rows = 90; # Cols = 1
After digging into this further, I found the problem was that the
tdof_filtered_func_data.nii.gz file in the cope1.feat subdir was the
wrong size.
I have 16 subjects, and there are 6 COPES in this experiment. I
therefore expect
the intermediate merged files in the gfeat/cope1.feat dirs to have
16*6 = 96 vols.
And indeed this is the case for merged cope and varcope files:
avwinfo filtered_func_data.nii.gz | grep "^dim4"
dim4 96
avwinfo var_filtered_func_data.nii.gz | grep "^dim4"
dim4 96
but not for the tdof file:
avwinfo tdof_filtered_func_data.nii.gz | grep "^dim4"
dim4 90
Q: Is this a bug or am I doing something wrong?
If so, what is the correct way of doing this?
(5) Finally, as sanity check I have:
(a) gone back to my simple group analysis explained in (2) above and looked at
it more carefully. The tdof mismatch is here too, and has presumably corrupted
my final output stats, but oddly it did not create any errors in the
report.log file.
filtered_func_data.nii.gz dim4 16
var_filtered_func_data.nii.gz dim4 16
tdof_filtered_func_data.nii.gz dim4 15
(b) rerun the factorial model using FSLv4 (FEAT 5.90). This causes similar
errors to be reported in cope1.feat/report_log.html
usr/local/fsl4/bin/flame --cope=tmpcope0 --vc=tmpvarcope0
--dvc=tmptdof0 --mask=tmpmask0 --ld=stats0 --dm=design.mat
--cs=design.grp --tc=design.con --fc=design.fts --ols
--nj=10000 --bi=500 --se=1 --fm --zlt=2.25 --zut=2.65
An exception has been thrown
Logic error:- detected by Newmat: index error: requested index = 91
MatrixType = Rect # Rows = 90; # Cols = 1
Trace: Mcmc_Mh::setup; Gsmanager::run.
And once again the volume sizes of the merged files are out of sync:
filtered_func_data.nii.gz dim4 96
var_filtered_func_data.nii.gz dim4 96
tdof_filtered_func_data.nii.gz dim4 90
It appears that the problem comes in the creation of the merged
tdof_filtered_func_data file. On creation of this file, the FEAT
analysis silently
drops the tdof volumes that should have been present from subject 1,
without any
warnings being generated. Presumably these are not created for first
level analyses,
and this is the real origin of the problem? In which case, I refer
back to my original
question about whether one can mix COPEs from different levels? And if so, how
best to do it?
Apologies for the long email but I hope I have explained the problem clearly.
Please advise!
kind regards
Sophie
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