Hi,
Try it without specifying the mask with the -m option and see if that works (keeping the --label still).
All the best,
Mark
On 3 Apr 2013, at 14:16, R. Ross MacLean <[log in to unmask]> wrote:
> Hi Andreas and Mark,
>
> re: Andreas - When I include"--label=mask_all.nii.gz" (without quotes) in the fslmeants syntax, the txt output is all zeros. If I use the same syntax without the label option and adding the "--showall" option I get activation time courses for each voxel within the mask. Therefore, I assume there is actual activation in the ROIs, but for some reason the "--label" option isn't extracting the time courses.
>
> re:Mark - The images are aligned correctly. If I open both the input and mask in FSLView there are non-zero values within each ROI and each ROI has a separate intensity value (i.e., 1-11). The ROIs are also located at the correct MNI xyz coordinates used to create the 8mm sphere.
>
> Thanks for your persistence.
>
> Best,
> Ross
>
> On Wed, 3 Apr 2013 08:09:52 +0000, Mark Jenkinson <[log in to unmask]> wrote:
>
>> 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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