I am stuck at extracting the BOLD signals of all the voxels within a mask from 4D NIfTI images in FSL. In FSL if we hover over a 4D fMRI image to any particular voxel and click it, then we can see the time-series data of that particular voxel which is our required BOLD signal of that voxel. But I want the time-series or BOLD signal data of all the voxels within the mask extracted at once. How do I do it in FSL or if there is any script that can help me solve this problem.
It would be very much helpful for any kind of help provided.
To do this you need to use the FSL utility fslmeants. This is a utility that you run from the command line. You can then import this average time series into fsleyes to display it (or any other graphing program).
R. Allen Waggoner: Thanks for responding to my query. I didn't know about fslmeants. I will surely look at it. I will update as soon as I have my problem resolved.
Hi Sumit, May I ask if you were able to resolve your problem using fslmeants function?
I did fslmeants -i rfMRI.nii -o output.txt where rfMRI.nii is my 4D nifti resting state file and its dimension is [79 95 79 427]. The text file this syntax outputs has 427 rows and one column while I need the to extract timeseries of all voxels. I was wondering if you know how I can do this. Any comment/help is appreciated!
Samaneh Nemati Your command is extracting the average timeseries for all voxels. You can use the --showall flag to extract the time series for each voxel and should produce a 592895 x 427 data matrix. I think you can modify your command like so: fslmeants -i rfMRI.nii --showall -o output.txt
Thank you so much Amber Howell for answering my question. I did what you suggested, but it seems the generated .txt file is too large to open it or to run analysis on it.
This is why you should use AFNI ;)
https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dmaskave.html
William Matchin , Thank you! Only if you could get AFNI working on a Windows machine! :)
You can use AFNI on Windows, by using WSL (Windows Subsystem for Linux). See https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_windows10.html
I had the same problem, and I need the time series data in every slice across the time.
Samaneh Nemati Did AFNI work for you?
Mahdi Mobarak Abadi I did not try AFNI, but I used a MATLAB script to do this and worked well. I can email you if you send your email address to me. I extracted time series for each ROI though. I do not know if it is what you aim to do.
Samaneh Nemati you can use fslmeants -i rfMRI.nii -o output.txt -m mask_roi.
fslmeants will give an average value of each time point within the binary mask/ROI which you have to create sepeartely. in the above code the mask created is mask_roi.
Or you can use the flag --showall to show all voxel time series (within mask) instead of averaging.
Hi Sumit,
If you use Matlab you can try the function 'grabTimesieries' which is part of a toolbox I have put online for reactivity mapping using BOLD data. You only need to pass the BOLD data and the mask and then it will return a list of all the voxel-timeseries along with their coordinates (so you can reformat them back into a 4D timeseries after processing, for example)
https://github.com/abhogal-lab/seeVR
- Badges
- Science topic
- Similar topics
- Correction