Got it. Thanks for the quick reply.
Vic
On Feb 10, 2013, at 10:10 AM, Matt Glasser <[log in to unmask]> wrote:
> 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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