Hi Mark, Thanks I did not know this. I included the correct syntax and the script ran without errors, but my text file output was full of zeros (presumably showing no activation within my ROIs, which I know to be untrue). I apologize for this thread being removed from my original question. I copied the original exchange with Steve Smith below. Any thoughts as to why I am getting all zeros.
The syntax I typed:
fslmeants -i <input file path> -m <path to image with 11 spherical ROIs> --label=<path to image with 11 spherical ROIs with labeled intensities 1-11> -o <path to output file> --transpose
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On Sat, Mar 30, 2013 at 4:47 AM, Stephen Smith <[log in to unmask]> wrote:
Hi - just type fslmeants to get the usage - sounds like you want the --label option?
Steve.
On 29 Mar 2013, at 22:56, R. Ross MacLean wrote:
Thanks Dr. Smith for the help; fslmeants does appear to be the correct tool. One additional question: if I use the "--showall" and "--transpose" I get the data for all voxels in my mask. How can I distinguish between ROIs? Is there a way to get the average time course from each ROI in a separate row? Alternatively can I use an option to distinguish between the voxel time courses for each ROI so I can average them in a separate program (i.e., MatLab or Excel)?
For clarity I entered
flmeants -i <input path> -m <mask path with 11 spherical ROIs> -o <output path> --showall --transpose
Thanks again!
Ross
On 28 Mar 2013 08:33:47, Stephen Smith wrote:
fslmeants
On 26 Mar 2013, at 21:33, R. Ross MacLean wrote:
Hi folks,
I am trying to extract individual activation time courses from 11 ROIs during a resting state scan. I created 11 spherical (8mm diameter) ROIs using xyz coordinates from another study. I gave each ROI a different intensity (1-11; using "-mul 0 -add 1, -mul 0 -add 2, etc when creating each ROI). Then I used the "fslmaths -add" to create one mask with all 11 ROIs. I believe I should use "featquery" however I am unsure how to implement it. I followed the directions on the FSL Featquery page, but when I apply the .feat directory in the gui, I do not get any stats images to investigate. Is this because it is resting state and I just have one .nii.gz image in the directory? Any help on how to extract individual time courses for each ROI would be much appreciated! Thanks in advance.
Best,
Ross
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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