Hi,
I was hoping you'd also include details about how you were resampling images and your fslmeants call.
You can check if things are appropriately registered by loading your sphereROI image into fslview and overlaying it on top of the input image you are using in fslmeants. If this looks right by eye then you should be OK to use fslmeants.
If you can't see the problem then please send us more details.
All the best,
Mark
On 17 Apr 2013, at 16:08, Nucleos P <[log in to unmask]> wrote:
> Hi,
>
> I followed these steps...
>
> I registered each subjects brain to the MNI152 brain first.
>
> 1) echo "X Y Z" | std2imgcoord -img
> $FSLDIR/data/standard/MNI152_T1_1mm -std
> $FSLDIR/data/standard/MNI152_T1_1mm -vox -
> 2) write down the numbers from step 1 (or store them in a variable
> using backquotes if you are familiar with that)
> 3) fslmaths $FSLDIR/data/standard/MNI152_T1_1mm -mul 0 -add 1 -roi A 1
> B 1 C 1 0 1 -kernel sphere 8 -dilF sphereROI
>
>
> I will investigate the registration issue further... It DOES seem very
> likely that this would be the cause.
>
> Thanks,
> Catherine
>
>
> On 4/17/13, zhang mingxia <[log in to unmask]> wrote:
>> Hi-According to my experience, it is easy to use the MNI coordinates which
>> is wrong. You should use the FSL coordinates. Also take care FSL
>> coordinates are different in 1mm and 2mm space.
>> Good luck.
>>
>> Mingxia
>>
>>
>> On Wed, Apr 17, 2013 at 5:21 AM, Mark Jenkinson <
>> [log in to unmask]> wrote:
>>
>>> 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
>>>
>>
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