On Fri, Nov 15, 2013 at 7:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Can you convert the two to mgz or nii with mri_convert and then run tkregister2? If they were acquired in the same session, then the geometric information in the header should bring them into close registration regardless of voxel size, orientation, field of view, etc. mri_convert should preserve this information. dcm2nii should do the same thing, but I did not write it so I don't know what it is doing:).

On 11/15/2013 01:15 PM, Martijn Steenwijk wrote:

Yes, they were acquired in the same session, but using a slightly different FOV. They were converted from dicom to nifti using dcm2nii and then used for FS analysis.

The axis orientation of the images is the same. Extensive image analysis (including registration of FLAIR and T1 using FLIRT) has been run on these images, but I never faced such a problem.

Is it possible that left/right orientation is is flipped by FLIRT due to the initial misalignment?

On Fri, Nov 15, 2013 at 6:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

were these acquired in the same session? If so, were they
converted to mgz directly from dicom?

On 11/15/2013 10:15 AM, Martijn Steenwijk wrote:

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
<mailto:martijnsteenwijk@gmail.com>
<mailto:martijnsteenwijk@gmail.com

<mailto: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
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu

<mailto: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
<mailto:martijnsteenwijk@gmail.com>
<mailto:martijnsteenwijk@gmail.com

<mailto:martijnsteenwijk@gmail.com>>>

>> Date: Thursday, November 14, 2013 9:27 AM
>> To: Bruce Fischl <fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>
<mailto:fischl@nmr.mgh.harvard.edu

<mailto:fischl@nmr.mgh.harvard.edu>>>
>> Cc: Veronica Popescu <v.popescu@vumc.nl
<mailto:v.popescu@vumc.nl>
<mailto:v.popescu@vumc.nl

<mailto:v.popescu@vumc.nl>>>, Hugo Vrenken
>> <h.vrenken@vumc.nl <mailto:h.vrenken@vumc.nl>
<mailto:h.vrenken@vumc.nl <mailto:h.vrenken@vumc.nl>>>,
>> freesurfer <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu

<mailto: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
<mailto:fischl@nmr.mgh.harvard.edu>
<mailto:fischl@nmr.mgh.harvard.edu

<mailto: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.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu

<mailto:greve@nmr.mgh.harvard.edu>>
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Outgoing:
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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