I think that must be experience from a long time ago, as you say -
FLIRT is rock solid ;-)
xxx
On 18 Mar 2008, at 18:49, Peter Kochunov wrote:
> Steve,
> You're absolutely right that this step is quite redundant as far as
> the end result goes.
> My experience with registering these modalities is that infrequently
> flirt crashes when it is faces with registering grossly different
> voxel spacing/array sizes.
> Now, this could have been a relict from the earler, less stable
> versions of the flirt. So, normally I just run an extra step that
> just resamples it into the proper spacings.
> pk
>
>
> ----- Original Message ----- From: "Steve Smith"
> <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Tuesday, March 18, 2008 12:36 PM
> Subject: Re: [FSL] White matter hyperintensity and FLAIR processing
>
>
>> Hi - I hate to disagree with PeterK (he has a much faster car than
>> I do and a much bigger spear-gun) but I don't think there's any
>> reason to upsample the FLAIR before feeding it into FLIRT. You can
>> just register it directly to the MPRAGE.
>>
>> Cheers, Steve.
>>
>>
>>
>> On 18 Mar 2008, at 17:26, Agnieszka Burzynska wrote:
>>
>>> Hi,
>>> My first plan was to do:
>>> 1)FLAIR-> resample to 1mm isovoxel-> to MPRAGE
>>> 2) MPRAGE->MNI
>>> 3) FLAIR->step 2 displacement field->to MNI space
>>>
>>> However, the resampled FLAIR looks, well, ...like FLAIR resampled
>>> from 5mm
>>> to 1mm :)
>>>
>>> Do you have any ideas and experience when can I do the resampling
>>> the
>>> latest?
>>> Is it better to use 1x1x1mm T1 image but from different scan or
>>> worse
>>> resolution scan from the same session? Does it make any
>>> difference for the
>>> FLIRT functions (if it needs to rotate the brain more, etc.)?
>>>
>>> Sorry to trouble you, but I am new to registration and dont have
>>> the
>>> "feeling" yet what is the best.
>>>
>>> Thanks a lot,
>>> Aga
>>>
>>>
>>>
>>> On 18.03.2008 17:02 Uhr, "Minjie Wu" <[log in to unmask]> wrote:
>>>
>>>> Hi,
>>>>
>>>> I think the registration from FLAIR image into MNI space can be
>>>> carried out in a hierarchical way
>>>> in FSL:
>>>> 1. FLAIR to MPRAGE, use rigid or affine registration , and produce
>>>> affined-transformed flair
>>>> 2. MPRAGE to MNI use nonlinear registration
>>>> 3. displacement field from step 2 can used to further transform
>>>> affined transformed flair into
>>>> MNI.
>>>>
>>>> Also there is a method for automated WMH segmentation and
>>>> localization.
>>>> " A fully automated method for quantifying and localizing white
>>>> matter
>>>> hyperintensities on MR images."
>>>> Psychiatry Research: Neuroimaging, Volume 148, Issue 2-3, Pages
>>>> 133-142
>>>>
>>>> Good luck,
>>>> Minjie Wu
>>>>
>>>> On Tue, Mar 18, 2008 at 11:45 AM, Peter Kochunov <[log in to unmask]
>>>> > wrote:
>>>>> I think you should have little troubles registering two
>>>>> datasets. One step
>>>>> you can do to insure stability is reslicing the FLAIR data into
>>>>> 1x1x1
>>>>> resolution before regestering it to T1w. Also you might want to
>>>>> play with
>>>>> the cost function in flirt. The normalized correlation don't
>>>>> seem to work as
>>>>> well as say mutual info.
>>>>>
>>>>> pk
>>>>> ----- Original Message -----
>>>>> From: "Agnieszka Burzynska" <[log in to unmask]>
>>>>> To: <[log in to unmask]>
>>>>>
>>>>>
>>>>> Sent: Tuesday, March 18, 2008 10:39 AM
>>>>> Subject: Re: [FSL] White matter hyperintensity and FLAIR
>>>>> processing
>>>>>
>>>>>
>>>>>> Dear Peter,
>>>>>> Thank you a lot for your email.
>>>>>> I can do without the automation (will do manual identification
>>>>>> of affected
>>>>>> tissue), but I would like to have my FLAIR images in the MNI
>>>>>> space. Do you
>>>>>> know if anyone does such registration with 5mm slice thickness?
>>>>>> I know you
>>>>>> had 1mm isovoxel in your recent study and others with my
>>>>>> parameters just
>>>>>> do
>>>>>> manual tracing on FLAIR image + multiply by slice gap to get
>>>>>> the WMH
>>>>>> volume.
>>>>>>
>>>>>> Do you know if I will get this registration well in FLIRT and
>>>>>> my MPRAGE or
>>>>>> shall I use a 1x1x1 T1-WI of these subjects (I may get them,
>>>>>> but acquired
>>>>>> in
>>>>>> different MRI session- or will it cause even more problems
>>>>>> with my FLAIR
>>>>>> quality?). I am not too familiar with FLIRT yet.
>>>>>>
>>>>>> Thanks a lot,
>>>>>> Aga
>>>>>>
>>>>>>
>>>>>> On 18.03.2008 14:33 Uhr, "Peter Kochunov"
>>>>>> <[log in to unmask]> wrote:
>>>>>>
>>>>>>> Aga,
>>>>>>>
>>>>>>> Unfortunatly, I don't think automated processing will be
>>>>>>> possible with
>>>>>>> this
>>>>>>> dataset. The only workable approach to do automated HWM lesion
>>>>>>> segmentation
>>>>>>> is by the use of T2-maps produced by the multi-echo sequences.
>>>>>>> pk
>>>>>>> ----- Original Message -----
>>>>>>> From: "Agnieszka Burzynska" <[log in to unmask]>
>>>>>>> To: <[log in to unmask]>
>>>>>>> Sent: Tuesday, March 18, 2008 7:09 AM
>>>>>>> Subject: [FSL] White matter hyperintensity and FLAIR processing
>>>>>>>
>>>>>>>
>>>>>>>> Dear all,
>>>>>>>> I am searching for the most straightforward way to estimate
>>>>>>>> the WMH load
>>>>>>>> in
>>>>>>>> my subjects.
>>>>>>>> 1) Was there any follow-up on the message from 2002? (see
>>>>>>>> below)
>>>>>>>> 2) My FLAIR images have resolution 1.3x0.9x5mm and my MPRAGE
>>>>>>>> 2x2x1mm.
>>>>>>>> Does
>>>>>>>> it mean I will have hard time in registering them to MNI?
>>>>>>>>
>>>>>>>> Thank you!
>>>>>>>>
>>>>>>>> Aga
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, 22 Jul 2002, Wei Wen wrote:
>>>>>>>>
>>>>>>>>> Dear Steve,
>>>>>>>>>
>>>>>>>>> It may be possible to extract (segment) white matter
>>>>>>>>> hyperintensity
>>>>>>>>> (FLAIR
>>>>>>>>> sequence) using a combination of bet, fast etc. as
>>>>>>>>> discussed at FSL
>>>>>>>>> course
>>>>>>>>> in Melbourne. Could I send you a couple of such images and
>>>>>>>>> see if you
>>>>>>>>> could
>>>>>>>>> tweak the programs (or come up with some suggestions) for
>>>>>>>>> this purpose?
>>>>>>>>>
>>>>>>>>> Many thanks,
>>>>>>>>>
>>>>>>>>> Wei Wen
>>>>>>>>> NPI, Prince of Wales Hospital/UNSW
>>>>>>>>> Australia
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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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