Hi,
--label=<input 3D label image (generate separate mean for each integer
label value..>
Cheers,
Andreas
Am 02.04.13 18:43 schrieb "R. Ross MacLean" unter <[log in to unmask]>:
>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
>
>-----------------------------------
>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
>
>
>--------------------------------------------------------------------------
>-
>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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