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Subject:

Re: Extracting multiple ROI time courses from one mask

From:

"R. Ross MacLean" <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 3 Apr 2013 14:16:03 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (134 lines)

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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