Hi All,
I am trying to replicate the methods from the Damoiseax 2008 Cerebral Cortex
paper, and thanks to Christian Beckmann and the other members of the list, I
am getting closer.
I have converted smoothed, normalized fMRI data of a resting state run
(TR2.5/300s/120vols) into power spectral information using fslpspec. This
results in 60 volumes representing different frequency bins written in a nii.gz
file (Christian posted how to calculate the bins - many thanks). I am having
difficulty running the TICA - the gica log said it wasn't converging at the PCA
step - so I backed up and tried to run single-session ica on one subject.
If I enter this data into melodic in FSL 4.0, the program seems to be
overwriting the nii.gz file, so that the power spectral data is lost. An error is
then thrown that either says that the PCA failed to converge or that the data
set is empty.
If I enter the data into melodic in FSL 3.2, it will run, but it usually results in
between 1-4 components that are not apparently biologically meaningful. We
also tried omitting the first volume of the spectral data, as it is very low
frequency and seems to have a lot of noise, but this did not change the
results.
I am wondering if I am entering the correct information into the GUI. I have
tried entering the actual TR and a TR of 0.0, running melodic with and without
functions like BET and MCFLIRT, and using various hpf or turning it off
altogether.
We are planning on Monday to try creating the power spectral data in another
way to see if there is a problem with the pspec files themselves, for some
reason, but I was wondering if anyone had had similar problems, or can see an
obvious mistake(s) that I am making.
Thank you so much for any advice you can offer! I am very interested to see
the results of this analysis.
Thanks,
Christina
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