It might be better to concatenate the data first in a single 4D file before
running melodic, as this isn't really "group" ICA. Then fsl_regfilt would
run properly on the output melodic_mix when you specify the components.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Koene Van Dijk
Sent: Tuesday, March 06, 2012 9:24 PM
To: [log in to unmask]
Subject: [FSL] UPDATE: Applying fsl_regfilt after melodic to denoise the
several 4D datasets.
In the meantime I have learned a little bit more about my melodic output.
Let me update my questions that I submitted yesterday:
If I run this command:
melodic -i list_of_4D_fMRI_datasets.txt --report -v --tr=5 --Oall -o
output.ica
...on 1 BOLD run of 90 volumes I get a file for the first component with 1
column with 90 entries:
./output.ica/report/t1.txt
If I run the same command but include 2 BOLD runs with each 90 volumes (i.e.
180 volumes) I will get a total of 3 columns in the "t1.txt" file. I see
that the number of columns is always: number of bold runs + 1.
I guess that there is one column for the time course of the respective
component for each run + one summary measure or so. I tried it with flag
"-a" set to default (=tica) and with concat which gave the same file
structure.
Can somebody tell me which column is which?
And what the +1 column represents?
Thanks,
Koene Van Dijk
PS: Here are the first 10 lines of such a file when I used two bold runs as
input (using tica)
head /output.ica/report/t1.txt
1.86719 1.90851 1.75934
1.72553 1.74516 1.6743
2.00228 1.65566 2.90701
1.71611 1.65537 1.87466
1.68615 1.71394 1.61362
1.61661 1.36676 2.26876
1.43963 1.50949 1.2573
1.88293 1.77197 2.17257
1.3938 1.35532 1.49425
1.3309 1.58513 0.667326
On Mon, 5 Mar 2012 17:18:27 +0000, Koene Van Dijk <[log in to unmask]>
wrote:
>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#d
enoising
>
>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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