Dear all,
I am using melodic on a single subject. I have multiple runs of resting state fMRI: 6 runs of 90 volumes each, i.e 540 volumes in total. I have already performed slice-timing correction and motion correction (all 539 volumes were registered to the first volume of the first run).
This is what I ran on my linux box using fsl 4.1.9 (64-bit):
melodic -i list_of_five_4D_fMRI_datasets.txt --report -v --tr=5 --Oall -o output.ica
It gives 25 components with beautiful maps. I now would like to remove some obvious noise components from the 4D data set and save the residual as new 4D dataset for other analyses.
On the following website I read about using fsl_regfilt:
http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/melodic/index.htm#denoising
And I tried this to remove components 1,2 and 3:
fsl_regfilt -i list_of_five_4D_fMRI_datasets.txt -d ./output.ica/melodic_mix -o denoise_ICAfiltered -f "1,2,3"
This does not work: "ERROR: cannot read input image".
So you can see that I entered my "list_of_five_4D_fMRI_datasets.txt" that I also used for the initial melodic command. I guess fsl_regfilt is not designed to take a list as input files, as melodic is.
My first question is:
1) Would anyone have a suggestion for how I can remove some components from this dataset using fsl_regfilt?
If I would like to regress out the components with another tool (any glm tool that allows me to save the 6 residual 4D fMRI runs), I would need to input the time course of the components. For example component 1, I found a text file here:
./output.ica/report/t1.txt
This file contains 90 rows and 7 columns. This surprised me because I was expecting to find 90 x 6 (=540) and not 90 x 7 (=630) values to represent the time course of component 1.
So my next questions are:
2. Why are there 90 x 7 columns and not 90 x 6?
3. Which time course would you recommend I take to use as regressor of no-interest if I would want to regress out a noise component?
Thanks a lot for any advice!
Best regards,
Koene
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