Hi Andreas,
I am not sure what you mean for the input syntax. Let's say right now I have "--label=mask_all.nii.gz" where mask_all.nii.gz is a 3D image file that contains all of my 11 spherical ROIs with separate intensities (1-11). I would like to do exactly what you stated in your response (i.e., generate a separate mean for each integer label value),do I simply put (generate separate mean for each label integer value.." in the syntax? I currently get all zero's in the output, so I am not sure that I have everything correct for the label option. When I run the syntax without the label option and use "--showall" I get time courses for each voxel (which can be tedious to work with). Thanks in advance for your willingness to offer help.
Best,
Ross
On Tue, 2 Apr 2013 20:05:53 +0200, Andreas Bartsch <[log in to unmask]> wrote:
>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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