Hi Steve,
I have uploaded the file again. The reference number is 336367.
A little more background information. This data is part of a 5 year
longitudinal study.
The images were collected on a 3T GE scanner. For the data from the
first four years,
Siena works great. All of the issues we see are after the scanner
software upgrade from the company. That is when we compare the pre-
and post upgrade images. We were reluctant to do any upgrades for the
scanner but we did not have full control over this issue. (The basic
argument was that it is hard to go 5 years or so without a scanner
software upgrade).
My feeling is that such issue would possibly come up for other
longitudinal studies too.
I was wondering if maybe some normalization pre-processing procedure
like histogram matching (after skull stripping) might help to
alleviate the problems.
Thanks
Mehul
Thanks
Mehul
On Fri, Sep 11, 2009 at 10:47 PM, Steve Smith <[log in to unmask]> wrote:
> Hi - the file you uploaded was empty - can you send it again?
> Cheers.
>
>
> On 10 Sep 2009, at 19:43, Mehul Sampat wrote:
>
>> Hi Steve,
>>
>> Thank you for your suggestions earlier.
>>
>> I found that after the scanner software upgrade there are intensity
>> changes and also the SNR is better in the post-upgrade images.
>>
>> Also as you suggested I ran SIENA with the -d option and was looking
>> at the intermediate outputs of Siena. I think because of the intensity
>> changes, the BET segmentation results look different for the pre- and
>> post software upgrade images.
>>
>> I was wondering if you could please give a look at the intermediate
>> output for one case, to see if the problem with the PBVC value is
>> being caused by the BET output ?
>> I uploaded the all of the intermediate output for one case at
>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi. The reference number is
>> 595458.
>>
>> If BET is the cause for the positive PBVC value, is there a way to
>> input different BET parameters (in the Siena script) for each of the
>> images?
>>
>> Thanks
>> Mehul
>>
>> On Sun, Sep 6, 2009 at 4:38 AM, Steve Smith <[log in to unmask]> wrote:
>>>
>>> Hi - there's a number of things that can have changed in your scanner
>>> upgrade that could cause this, including intensity effects and
>>> geometrical
>>> effects.
>>>
>>> In general we _strongly_ recommend against any acquisition changes during
>>> a
>>> longitudinal study, as you can never be sure that you will be able to
>>> remove
>>> the confounds caused by the change.
>>>
>>> In your case you will need to look into all the intermediate stages
>>> (outputs) of SIENA to try to track down where this confound is affecting
>>> estimates. If you use the -d debug option SIENA will leave a lot of
>>> intermediate stages for you to look at.
>>>
>>> Cheers.
>>>
>>>
>>> On 5 Sep 2009, at 08:20, Mehul Sampat wrote:
>>>
>>>> Hi FSL Experts,
>>>>
>>>> I am using Siena to compute PBVC for MS patients.
>>>> In the past we would see a mean -0.4% PBVC value for two scans a year
>>>> apart.
>>>>
>>>> Recently, our GE scanner went through a software upgrade.
>>>> I am now comparing two scans (pre- and post- upgrade) using Siena.
>>>> (These pre- and post-upgrade images are also a year apart)
>>>> Strangely for many of the subjects, the PBVC values are now positive
>>>> (which is not what we expect for these patients).
>>>>
>>>> I tried Siena version 2.6 and version 2.4 and for both versions I see
>>>> positive PBVC value.
>>>> Has anyone experienced similar issues with Siena ? If so any
>>>> suggestions to overcome this issue would be very helpful.
>>>>
>>>> Also any suggestions on debugging the intermediate steps would also be
>>>> very helpful.
>>>> Thank you,
>>>> Mehul
>>>>
>>>
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> Stephen M. Smith, Professor of Biomedical Engineering
>>> Associate Director, Oxford University FMRIB Centre
>>>
>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>> +44 (0) 1865 222726 (fax 222717)
>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>
>>> ---------------------------------------------------------------------------
>>>
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
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