 |
 |
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 >>>>> -------------------------------------------------------------------------- >>>>> -