Hi Ross,

and  "--label=mask_all.nii.gz" (without the quotes) does not work for you?
Cheers,
Andreas



Am 03.04.2013 um 01:45 schrieb "R. Ross MacLean" <[log in to unmask]>:

> 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
>>> --------------------------------------------------------------------------
>>> -