I digged further into this.

The scale difference previously reported is not true. It is only a translation error. 

It looks like that the orig.mgz has (0,0,0) in the center of the image; while FLAIRraw (after header-only registration) has the origin at index (0,0,0) - so in one of the corners of the volume. This means the initial (header based) transformation provided to flirt is also not correct.


On Fri, Nov 15, 2013 at 12:49 PM, Martijn Steenwijk <martijnsteenwijk@gmail.com> wrote:

Dear all,

Thanks for all the input. Doug, concerning your suggestion 
tkregister2 --mov FLAIRraw.mgz --targ orig.mgz --regheader --reg junk

Using this, the axes orientationseem to be correct, but scaling and translation of registered FLAIRraw seem to be way off. (registered FLAIRraw is much larger compared to orig.mgz (in the order of multiple times) and is translated to the radiologically left-caudal part of orig.mgz. 

mri_convert -rl gives a similar result as using tkregister2 as proposed by Doug. 

Best,
Martijn


On Thu, Nov 14, 2013 at 8:38 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

It should not make a difference. We compute an initial registration
based on the header and pass that to FLIRT. Can you verify that this
initial registration is correct? You can do that with

tkregister2 --mov FLAIRraw.mgz --targ orig.mgz --regheader --reg junk

If that looks ok, then it is possible that flirt is just failing.

Also, newer versions of FS will use an internal version of flirt and so
not reliant on FSLDIR being set or FSL being installed.

doug




On 11/14/2013 12:52 PM, Bruce Fischl wrote:
> Hi Matt
>
> hopefully Doug will chime in, but I don't see why that is the case. We
> preserve all the RAS information when we "conform", so the info should
> be there for flirt
>
> cheers
> Bruce
>
>
> On Thu, 14 Nov 2013, Matt Glasser wrote:
>
>> I think you can do it with mri_convert ?rl.  I don't think it makes
>> sense to
>> expect FLIRT to get the registration right reliably if the axes are
>> off (in
>> the HCP Pipelines we definitely don't expect this and make sure all
>> images
>> are RPI before processing them).
>>
>> Peace,
>>
>> Matt.
>>
>> From: Martijn Steenwijk <martijnsteenwijk@gmail.com>
>> Date: Thursday, November 14, 2013 9:27 AM
>> To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
>> Cc: Veronica Popescu <v.popescu@vumc.nl>, Hugo Vrenken
>> <h.vrenken@vumc.nl>,
>> freesurfer <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] T2pial/FLAIRpial processing issues
>>
>> Hi Matt, Bruce,
>> The problems are indeed a flirt issue, but given that it's programmed
>> with
>> --init-fsl there is not much flexibility.
>>
>> However, from a FS point of view, it might be a better and more robust
>> approach to first register FLAIRraw.mgz to raw.mgz, and then
>> concatenate the
>> resulting registration with the (header based) registration from
>> raw.mgz to
>> orig.mgz - instead of trusting the robustness of either registration
>> algorithms.
>>
>> ... or, as Matt suggests, fix the image axes appropriately after
>> converting
>> the FLAIR to mgz, and then run the registration. But I'm not sure how
>> to do
>> that.
>>
>> Best,
>> Martijn
>>
>>
>> On Thu, Nov 14, 2013 at 5:53 PM, Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu>
>> wrote:
>>       Hi Martijn
>>
>>       we can print warning and errors if FSLDIR is not set, but the
>>       registration errros seem to be mostly a flirt issue, no? Have
>>       you posted on the FSL list?
>>
>>       Bruce
>>
>>       On Thu, 14 Nov 2013, Martijn Steenwijk wrote:
>>
>>             Dear all,
>>             There seem to be some serious issues with the T2pial
>>             / FLAIRpial processing
>>             options provided in the latest versions of
>>             FreeSurfer.
>>
>>             First of all, although not clearly documented,
>>             T2pial / FLAIRpial processing
>>             does require the FSLDIR to be set (in order to use
>>             bbregister with
>>             --init-fsl). If not set,  recon-all will
>>             finish just without using the T2 or
>>             FLAIR information. Importantly, no clear warning
>>             about this is given
>>             although the user expects that T2/FLAIR has been
>>             used for pial surface
>>             refinement. I think this is a very easy source of
>>             errors, so it might be a
>>             good idea to just throw an error when FSLDIR is
>>             missing and T2pial/FLAIRpial
>>             processing is requested.
>>
>>             Second, if FSLDIR has been set. T2pial/FLAIRpial
>>             uses bbregister with FLIRT
>>             initialisation to align the T2 or FLAIR image to
>>             orig.mgz. However, we have
>>             some high-res 3DFLAIR data in which this
>>             registration (more specifially, the
>>             FLIRT initialisation step of bbregister) seems to
>>             fail in more than half of
>>             the cases. Apparently, the FSL initialisation is not
>>             capable to change the
>>             orientation such that it fits to the coordinate
>>             system used for orig.mgz.
>>             Again, no warning or error is thrown, but the
>>             processing just continues with
>>             the wrong registration and without noticing the
>>             results will get worse
>>             compared to not using T2 or FLAIR.
>>             Although I know its essential to look at the output
>>             data; would it be
>>             possible to put some effort in letting the user know
>>             that things got wrong?
>>
>>
>>             As a sidenote; I tried to fix this registration
>>             issue, but it seems to be
>>             very complicated using bbregister (other than just
>>             inserting my own
>>             registration obtained by using FLIRT to register
>>             native FLAIR to native T1,
>>             and subsequently transform the result to Freesurfer
>>             space in order to obtain
>>             FLAIR.mgz).
>>
>>             Best,
>>             Martijn
>>
>>
>>
>>
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Douglas N. Greve, Ph.D.
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greve@nmr.mgh.harvard.edu
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