Having problems with the JISCMail, so trying my luck here:
How can I regress out nuisance regressors (WM, CSF signal, motion and global mean outliers) without having a model or main EVs because my data is a 6min resting state scan? I want to regress out the unwanted signal and then have a new clean filtered_func_data.nii.gz to use for time series extraction of ROIs. As I understood frm the literature regressing out nuisance as a preliminary step cna be done, but HOW it is done especially with FSL I couldnt figure out.
I have it all in one combined txt file with all nuisance regressors which I tried uploading under confound EVs, but I didnt know what to do about the model set up and all the other options.
A step by step guidance through setting up the regression would be much appreciated.
thank you! so what is the output you get and howndo you check whether it worked?
I got the following answer on JISCMail:
Hi Val, hi Bob,
To regress out a set of nuisance variables use the command fsl_glm. Something as this:
fsl_glm -i filtered_func_data.nii.gz -d design_with_nuisance.mat --out_res=filtered_func_data_new.nii.gz
The filtered_func_data_new.nii.gz are the residuals of the model that has these variables, hence will be free of these nuisance effects.
If there are hundreds of timepoints and only a few nuisance variables regressed in this way, it's fine. However, if there are only a few observations and too many variables, this procedure will cause false positives later, because the residuals are no longer independent, and the true degrees of freedom of the subsequent model will be overestimated.
All the best,
Anderson
Hi!
I am not sure how to do it myself. So the nuisance_design.mat is that an output of a setup design by feat or is it just a file with vectors of timeseries to be regressed out. I have the timeseries of the nuisance as a .txt, I had a WM.txt and CSF.txt and ART output including both motion and global mean putliers in one file, say art.txt then I combined the three txt files into nuisance.txt with bash script command paste. I guess from there one can convert the txt file into a .mat. Question is, is that correct procedure of do I need to set up FEAT beforehand and use FEAT output for fsl_glm? You are welcome to ask you follow up questions directly, here is the link to my question:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1605&L=FSL&F=&S=&X=124BE7CBB64104BC29&Y=v.azorina%40gmail.com&P=170979
what is you motion file? .par? may be it is also possible to convert it to .txt and add all three files together?
Unfortunatelly, I am no expert on that either, it"s my first resting state analysis.May be you should ask it as a follow up question in JISCMail. I will try out your procedure from above now. Thanks!
Hi!
I am trying to regress out WM, CSF and also the 24 regressors constructed from the 6 that I have in the .par file.
I managed to extract the time course for CSF and WM, so now I have a .txt file for each one. My problem is that I don't know how I could get the derivatives from the 6 motion parameters I have to generate 12 and then 24 regressors.
I also don't know how to regress these out from the data once I have everything I need.
Did you find some answers to this problem?
Thank you so much!
Hi,
It may be a bit late. But this may help you. I came across this question for a while and just asked for help in the FSL email list. The result from fsl command (with adding a column of 1's in the design matrix) is very close to the result I ran in Matlab (via the least square solution)
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2010&L=FSL&P=R139262&X=0354F3B77F77E32D32&Y=junlin.guo%40vanderbilt.edu
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