Hi Jeff
This is then probably a question for the FreeSurfer list. I do not know what difference they may have introduced into their bedpostx calls.
Cheers
Stam
On 7 Feb 2014, at 14:43, Harms, Michael <[log in to unmask]> wrote:
> Hi Jeff,
> 5.1 and 5.3 are FreeSurfer versions. If you are using a version of
> bedpostx embedded in the FreeSurfer distribution, then for Stam to be
> helpful you'll probably need to identify the FSL version of bedpostx
> included in each of those.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: [log in to unmask]
>
>
>
>
> On 2/7/14 8:37 AM, "Jeff Waugh" <[log in to unmask]> wrote:
>
>> Hi Stam,
>> By 5.1 etc. I mean that I source the local environment (currently =
>> source /usr/local/freesurfer/nmr-stable53-env). Bedpostx runs that were
>> run in the current environment twice have some variability, as you
>> said, but not much. Between the earlier (5.1) and current versions the
>> variability is larger. To compare the versions I just did a fslmaths
>> subtraction to generate a "difference map", then looked at this
>> difference map relative to the original image. For the 3-4 subjects
>> I've looked as so far, the current environment generates a slightly
>> larger file, with greater intensities at most (but not all) voxels.
>>
>> Thanks,
>> Jeff
>>
>>
>>> Hi Jeff
>>>
>>> I am not sure I understand what the versions 5.1 or 5.3 are. Are you
>>> referring to different FSL versions (in which case this is 5.01 and
>>> 5.03)
>>> or to different system versions of your operating system or scanner
>>> software?
>>> Notice that bedpostx is probabilistic, so there will be a variability in
>>> the results. How do you assess this 10-20% variation? Is this on
>>> average,
>>> across the whole f1 map?
>>>
>>> Cheers
>>> Stam
>>>
>>>
>>> On 6 Feb 2014, at 21:05, Jeff Waugh <[log in to unmask]> wrote:
>>>
>>>> Hello all,
>>>>
>>>> I have run bedpostx on a series of DTI scans over ~1 year. In that
>>>> time, my center upgraded it's standard command line operations (MGH
>>>> Martinos Center, stable 5.1 to (current) stable 5.3). I'm seeing quite
>>>> a lot of variability in intensity from the earlier to later versions -
>>>> re-running bedpostx in 5.3 on an older scan and comparing with 5.1
>>>> yields a 10-20% variation in intensity between versions. I've been
>>>> comparing the mean_f1 images. Has anyone else seen this?
>>>>
>>>> Thanks,
>>>> Jeff
>>>>
>>>>
>>>>
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