Hi,

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,
   Mark

wolf zinke <[log in to unmask]> wrote:


Hi,

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
brain.

good luck,
wolf

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
> values.
>
> Thank you,
> Cat
>
>
> On 4/15/13, wolf zinke <[log in to unmask]> wrote:
>> Hi,
>>
>> 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:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;6ce4bff3.1301
>>
>> I hope this helps,
>> wolf
>>
>> 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,
>>> Cat