Got it! Thanks so much!
Mingxia
On Tue, Jul 7, 2015 at 6:06 PM, paul mccarthy <[log in to unmask]>
wrote:
> Hi Zhang,
>
> You can use fslinfo to get the x/y/z dimensions (and t, if it is a 4D
> image):
>
> fslinfo <my_image>
>
> To calculate the total number of voxels, just calculate dim1 * dim2 * dim3
> * dim4
>
> Cheers,
>
> Paul
>
> On 7 July 2015 at 10:54, zhang mingxia <[log in to unmask]> wrote:
>
>> Hi Paul,
>>
>> Thank you for replying me! Another question: How do I know the total
>> number of voxels in an image?
>>
>> Mingxia
>>
>> On Tue, Jul 7, 2015 at 4:35 PM, paul mccarthy <[log in to unmask]>
>> wrote:
>>
>>> Hi Zhang,
>>>
>>> You can do this using fslstats - first, calculate the proportion of 100
>>> voxels relative to the total size of your image:
>>>
>>> prop = 100 / <total number of voxels in your image>
>>>
>>> Then use fslstats to find the percentile value at this proportion:
>>>
>>> fslstats <my_image> -p <100 - 100 * prop>
>>>
>>> (Use '-a' before '-p' if you are interested in absolute values)
>>>
>>> You can then use this percentile value as a threshold in fslmaths, to
>>> create a mask containing the 100 voxels with the highest intensity:
>>>
>>> fslmaths <my_image> -thr <threshold_from_fslstats> -bin <my_mask>
>>>
>>> Cheers,
>>>
>>> Paul
>>>
>>> On 7 July 2015 at 07:01, zhang mingxia <[log in to unmask]>
>>> wrote:
>>>
>>>> Hi Iwo,
>>>>
>>>> I don't want to creat a sphere ROI. I want the 100 voxels with the
>>>> largest z value in zstat.nii.gz to be the ROI mask. My question is how to
>>>> find out the 100 voxels with largest z value in zstat.nii.gz?
>>>>
>>>> Thank you again!
>>>>
>>>> Mingxia Zhang
>>>>
>>>> On Mon, Jul 6, 2015 at 7:28 PM, Iwo Bohr <[log in to unmask]> wrote:
>>>>
>>>>> Sorry, one correction to the previous message: the coordinates of the
>>>>> ROI central point are expressed in voxels, not in mm! (see below)
>>>>>
>>>>> Iwo
>>>>>
>>>>>
>>>>> ----- Forwarded Message -----
>>>>> *From:* Iwo Bohr <[log in to unmask]>
>>>>> *To:* [log in to unmask]
>>>>> *Sent:* Monday, 6 July 2015, 12:22
>>>>> *Subject:* Re: [FSL] making mask of a fixed number of voxels of the
>>>>> most responsive ones
>>>>>
>>>>> In terms of creating your ROI these two commands could be helpful:
>>>>>
>>>>> 1) fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm -mul 0 -add 1
>>>>> -roi $c1 1 $c2 1 $c3 1 0 1 ${out}point -odt float
>>>>> 2) fslmaths ${out}point -kernel sphere $rad -fmean ${out}$name -odt
>>>>> float
>>>>>
>>>>> where:
>>>>> $c1-$c3 are x,y,z coordinates (voxels) of the centre
>>>>> $rad : to replaced by the radius (mm)
>>>>>
>>>>> The above is for creating a ROI in the MNI space, but it could be
>>>>> replaced by any space.
>>>>> First command creates the centre of the ROI, second the spherical ROI
>>>>> (centred around the point).
>>>>>
>>>>> Hope this helps,
>>>>>
>>>>> Iwo
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------
>>>>> *From:* zhang mingxia <[log in to unmask]>
>>>>> *To:* [log in to unmask]
>>>>> *Sent:* Monday, 6 July 2015, 10:39
>>>>> *Subject:* [FSL] making mask of a fixed number of voxels of the most
>>>>> responsive ones
>>>>>
>>>>> Dear FSL experts,
>>>>>
>>>>> I need to create a mask of the most responsive voxels. Specifically,
>>>>> in my study , I got the z value image of one condition (e.g.,
>>>>> zstat1.nii.gz). Now, I need to create a mask of a fixed number of
>>>>> voxels(e.g., 100) with max z value in zstat1.nii.gz. Does any one know how
>>>>> I can do?
>>>>>
>>>>> Thanks in advance!
>>>>>
>>>>> Mingxia Zhang
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
