Hi Mark -
Viewing the images over the MNI152_T1_1mm template in fslview, they
appear to be registered correctly and there is an intensity value at
my proposed ROI coordinates...
So when I open the sphereROI image it does not appear and all
intensity values are 0...?
fslmeants -i all_subjects_registered.nii.gz -m sphereROI -o ROI_values
Thank you,
Catherine
On 4/17/13, Mark Jenkinson <[log in to unmask]> wrote:
> 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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