Hi Mark,
That worked! Thanks so much for your help troubleshooting this. I hadn't thought to remove the mask option, but when I do I get the activation time courses for all 11 ROIs. Thanks again!
Best,
Ross
On Wed, 3 Apr 2013 23:02:11 +0000, Mark Jenkinson <[log in to unmask]> wrote:
>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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