Hi,
Are you sure the images are aligned correctly?
If you load both (mask_all and the input image) into FSLView - do you see non-zero values inside the ROIs within the input image?
All the best,
Mark
On 3 Apr 2013, at 09:20, Andreas Bartsch <[log in to unmask]>
wrote:
> 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
>>>> --------------------------------------------------------------------------
>>>> -
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