Hi,
I'm fairly new to FSL and I've been following this post in order to extract time course data from 15 ROIs.
I followed Ross' command to create labeled ROIs but when I opened them up in fslview, it was blank. Since that didn't work for me, I used the following command to label the masks:
fslmaths <input mask> -bin -mul <1, 2, 3, etc> <output labeled mask>
This file was visible in fslview with an intensity that matched the number it was multiplied by. I proceeded to make a composite mask of the 15 ROIs with the "fslmaths -add" command and each ROI had the correct label when I viewed the composite on fslview.
I converted this mask to each subjects native space, used the following command: fslmeants -i <input> --label=<composite_mask> --transpose -o <output>; and graphed the values for each subject. Every graph looked practically the same (which doesn't seem to be representative of the processed data). All work was double checked to make sure it was correct. I think the problem has to do with the labeled composite mask because I've selected single ROIs to rerun the above process and had different output values. Can anyone shed some light as to what I'm doing wrong?
Also, when running fslmeants, is it valid to use files other than the filtered_func_data, such as a cope file, or a thresh_zstat file? If so, what exactly do the output values for each of these files represent (e.g, are the outputs for the cope files the intensities above and below a baseline?)? Also, would it be ok to run this on group data?
Thanks in advance!
Best,
Eleni
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