Not cropping the images guarantees that the output averaged image has
exactly the same dimensions as the input image. This is important if you
want to compare the average image to the original images in a tool like
FSLView that is limited to viewing images of identical matrix dimensions.
Peace,
Matt.
On 2/10/13 11:48 AM, "Victor Schinazi" <[log in to unmask]> wrote:
>Hi Matt (or anyone else)- I am using the AnatomicalAverage script to
>average 2 T1 images. Can you tell me a little more about the option not
>to crop images (-n) and where it applies.
>
>Thank you,
>
>Victor Schinazi
>
>On Jan 30, 2013, at 6:22 PM, Matt Glasser <[log in to unmask]> wrote:
>
>> You can use AnatomicalAverage, a script Mark wrote for the HCP but has
>> also included in the FSL distribution.
>>
>> Peace,
>>
>> Matt.
>>
>> On 1/30/13 8:02 PM, "Vincent Koppelmans" <[log in to unmask]> wrote:
>>
>>> Could anybody please comment on this?
>>>
>>> Help is greatly appreciated.
>>>
>>> Thanks!
>>>
>>> Vincent
>>>
>>>> Dear Mark,
>>>>
>>>> Thank you for your answer. I was wondering what the best way would be
>>>> to average these images. Would you choose option A, B, or something
>>>>else?
>>>>
>>>> A) Rigid (6 DOF) registration of image B to image A. Subsequently add
>>>> (fslmaths -add) and average the two images (fslmaths -div 2).
>>>>
>>>> B) Average raw T1_A and T1_B. Rigid (6 DOF) registration of image T1_A
>>>> and T1_B to the raw mean image. Average the registered images.
>>>>
>>>> To me, option B seems like the most fair one, as it rotates and
>>>> translates both scans a little bit, and not only one scan the full
>>>> amount.
>>>>
>>>> What do you suggest?
>>>>
>>>> Thanks for your help,
>>>>
>>>> Vincent
>>>
>>>
>>>>> Yes!
>>>>>
>>>>> All the best,
>>>>> Mark
>>>>>
>>>>> On 24 Jan 2013, at 15:45, Vincent Koppelmans <[log in to unmask]>
>>>>>wrote:
>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I have a large dataset of T1-weighted images. Each subject has been
>>>>>> scanned twice with not much more than 45 min in between two scan
>>>>>> sessions.
>>>>>>
>>>>>> I was wondering if I it would make sense to co-register and average
>>>>>> these images to increase the SNR (and eventually get a better
>>>>>> segmentation).
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Vincent
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