i forgot to mention that i am running FSL v3.1.
> The "zeroing" of the zstat image isn't happening
> at the point with avwmaths that you suggest; it is happening
> in the cluster (thresholding) command slightly later,
oh, yes, i see that now. i did not expect the volume thresh_zstat1
to be both input and output to program cluster. it is good to know
that avwmaths -mas is not doing anything unexpected.
> it's just because this person isn't activating sufficiently
> strongly according to your design.
i see. thank you. in fact, if i change the p-threshold from
0.01 to 0.1 i start to see some activation.
> However, MELODIC does give plenty of visual activation,
yes, thank you for pointing this out -- an example of how ICA can
be of help.
i see the default threshold value for mixture model inference is 0.5,
ie, --mmthresh="0.5", whereas the p-threshold value for the cluster
program is -p 0.01. are these options equivalent between the two
programs? in fact, if i run the cluster program with
-p 0.5 --connectivity=26, i see activation.
also, is it appropriate to run MELODIC from the resulting
filtered_func_data volume created by FEAT while simultaneously
turning off the [Pre-stats] analysis? i turned off slice timing
correction, motion correction, BET, and spatial smoothing as i
did this in the FEAT analysis. i did leave on temporal filtering,
however, even though this was done in FEAT, too. i am a bit
inconsistent here so perhaps i should turn off temporal filtering,
> so it may just be that your model isn't a great one?
the timing file is based on the ePrime file that presents the
stimuli. looking at the responses of this subject, she responds
correctly 60% of the time so she is participating. stimuli are
presented for 1500ms and her mean response time is 880ms
(stdev 172ms). i computed the correlation between the ePrime
paradigm timing and each of the components found by MELODIC.
the correlations are very poor, [-0.1, 0.1]!!, which agrees with
no activation via GLM using the same ePrime paradigm timing file.
thank you for all the help and reality-checks,
BettyAnn Chodkowski F.M. Kirby Center
e: [log in to unmask] Kennedy Krieger Institute
v: 443.923.9524 707 N. Broadway
f: 443.923.9279 Baltimore, MD, USA 21205