I agree with Wolf that it may well be a registration issue, with images in the wrong spaces. It would be helpful if you could post the exact commands that you were running.
All the best,
wolf zinke <[log in to unmask]> wrote:
Maybe this is a problem with the transformation into the individual
subject brain space? Otherwise it might be a good idea to mask the
spherical ROI with a brain mask to ensure that it is not exceeding the
On 04/16/2013 08:28 PM, Nucleos P wrote:
> Hi Wolf -
> This helps...however, when I run fslmeants using the ROI sphere mask
> it shows all zeros for individual subjects. I've done more constrained
> analysis on the same image (e.g. less than 8mm radius) and gotten
> Thank you,
> On 4/15/13, wolf zinke <[log in to unmask]> wrote:
>> fslroi uses voxel, but would not be the right tool for your purpose
>> anyway, since it changes the image size, cropping it to the defined region.
>> If you want to create a cubic mask you can use the -roi option of
>> fslmaths. This option uses voxel coordinates, so you have to adjust the
>> values according to your voxel dimension.
>> If you want to create a more sphere-like ROI you can do follow this
>> description in a recent post:
>> I hope this helps,
>> On 04/16/2013 12:52 AM, Nucleos P wrote:
>>> Hello Experts -
>>> When using fslroi it is unclear if the x size, y size, and z size
>>> refer to mm or # of voxels around the coordinates?
>>> For instance, if I wanted to create a mask at ROI 125, 97, 107 MNI 152
>>> voxel coordinates and then extend to points outside (e.g. 8mm) how
>>> would I set this up?
>>> Thank you,