[Mrtrix-discussion] Question about filter_tracks command

Sun Jan 12 16:52:46 PST 2014

Hi Robert,

Regarding your advise to use the inverse phase method, how hard would it be
to implement? We use a Philips scanner and the first issue is to create the
sequence that gets the reverse phase. The second, however, is related on
how to apply that for correction. I haven't found any clue on the tools
that can perform the inverse phase correction.

Thank you.
Dorian
TJU

2014/1/12 Robert Smith <r.smith at brain.org.au>

> Hi Dan
>
> No worries at all; it can take a little while to wrap your head around
> having things operate in scanner space, most people are used to either
> voxel coordinates or MNI space; but for multi-modality per-subject data it
> makes a lot of sense.
>
> As long as the seed image 'overlaps' with the diffusion data in scanner
> space, then yes, a ROI drawn on the anatomical image can be used directly
> in streamtrack; it doesn't matter if the voxel grids are oriented
> differently with respect to the scanner axes, or the voxel sizes are
> different. The overlay tool in MRview is handy for assessing image
> alignment in such circumstances. I will raise two more points here however:
>
>    1. At least some form of image registration is required, to account
>    for inter-sequence subject motion and/or scanner re-calibration. Personally
>    I register the anatomical image to the diffusion images before deriving any
>    other images (e.g. seeding masks) from it; that way, all derived images
>    have the same header transform as the anatomical image, and therefore also
>    align with the diffusion data in scanner space. Alternatively, you can use
>    the transform derived from registration and apply it to the relevant ROI as
>    you have been, but omit the step where the ROI data is re-gridded to match
>    the diffusion images.
>    2. Due to the presence of susceptibility-induced geometric distortions
>    in EPI, a simple linear transform (whether rigid-body or affine) is
>    generally not adequate to achieve good alignment between the structural and
>    diffusion images. Therefore, although you can in principle use a
>    high-resolution seed image, in reality the anatomical structure you have
>    delineated in the high-resolution image may not map to the correct
>    anatomical location in the diffusion images, unless you have explicitly
>    performed susceptibility distortion correction. Personally I am a big
>    advocate of the reversed phase-encode method for estimating the
>    inhomogeneity field and subsequently correcting for these distortions, and
>    always recommend to people that they should commence acquiring the relevant
>    data in all of their studies.
>
> With regards to tracks2prob, as long as the T1 and diffusion image data
> overlap in scanner space, then again yes, you can use the T1 image as the
> template image for tracks2prob. You can even use both the -template and
> -vox options in conjunction to produce a TDI where the voxel grid is
> aligned with that of the T1 image, but the voxel size is smaller.
>
>
> Happy tracking!
> Rob
>
>
> --
>
> *Robert Smith, Ph.D*
> Research Officer, Imaging Division
>
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7128
> Fax: +61 3 9035 7301
> www.florey.edu.au
>
>
> On Mon, Jan 13, 2014 at 6:14 AM, Daniel Lumsden <doclumsden at hotmail.com>wrote:
>
>> Rob
>>
>> Thank you for a very helpful answer - apologies for slow acknowledgement
>> and reply!
>>
>> Given that mrtrix generates streamlines in "real space", does this mean
>> that I could create a seed region from an anatomical image converted from
>> the dicom to nifti using mrconvert, then supply that mask directly to
>> streamtrack?
>>
>> I've been creating mask images from reasonably high resolution T1 images,
>> then using the linear transform generated by flirt in FSL (transform of
>> structural scan to diffusion scan) to transform these mask images into the
>> much lower resolution diffusion space.
>>
>> If I can supply the seed directly, could I then use my T1 image as the
>> template for tracks2prob to visualise the track density on the scans
>> without needing to apply any transformation?
>>
>> I hope this isn't a hopelessly naive question!
>>
>> Dan
>>
>> ------------------------------
>> Date: Sun, 22 Dec 2013 10:37:52 +1100
>> Subject: Re: [Mrtrix-discussion] Question about filter_tracks command
>> From: r.smith at brain.org.au
>> To: doclumsden at hotmail.com
>> CC: mrtrix-discussion at www.nitrc.org
>>
>>
>> Hi Dan
>>
>> If you use the -template option in tracks2prob with the FA image as the
>> template, then yes, the transformation (at least the orientation component)
>> will be identical to the FA image. The offset component of the transform
>> will differ slightly if the voxel size is different in the TDI.
>>
>> This question does however raise an important difference between MRtrix
>> and other packages. The streamlines are generated and stored in 'real' /
>> 'scanner' space, rather than with respect to any particular image space. To
>> read an image value at a particular streamline position, the location is
>> mapped according to the transform of that particular image. Therefore, it
>> is not actually necessary for the ROI to be 'in the same space' (i.e. on
>> the same voxel grid) as the image used to generate the streamlines; as long
>> as the images are correctly aligned / registered, the streamline position
>> in scanner space can be transformed to the appropriate location in the
>> image volume.
>>
>> Theoretically, you could have a ROI based on the FA image, a ROI based on
>> the high-resolution TDI, and a ROI based on a (co-registered) anatomical
>> image, and they could all be used in the same call to filter_tracks.
>>
>> So if the purpose of the TDI is to identify a particular pathway and draw
>> a ROI, it doesn't actually matter whether or not the -template option is
>> provided to tracks2prob; the TDI will always be inherently aligned with the
>> streamlines data, regardless of the alignment of the voxel grid. Though as
>> an aside, you'll find the TDI file size will be much smaller if the
>> -template option is *not* used, as it then uses the streamlines data to
>> determine the required spatial extent of the image, so you don't get as
>> much 'dead space' around the brain.
>>
>> Happy holidays all
>> Rob
>>
>>
>> --
>>
>> *Robert Smith*
>> Post-Doctoral Researcher, Imaging Division
>>
>> The Florey Institute of Neuroscience and Mental Health
>> Melbourne Brain Centre - Austin Campus
>> 245 Burgundy Street
>> Heidelberg Vic 3084
>> Ph: +61 3 9035 7128
>> Fax: +61 3 9035 7301
>> www.florey.edu.au
>>
>>
>> On Sun, Dec 22, 2013 at 4:55 AM, Daniel Lumsden <doclumsden at hotmail.com>wrote:
>>
>> Dear All
>>
>> I'm interested in using the improved resolution from track density images
>> to help improve my ROI generation to select tracks from a whole brain
>> tractography .tck file.
>>
>> I can define, e.g., the PLIC much more sharply from the track density
>> image generated from whole-brain tractography much more easily then from
>> the standard colour coded FA maps. The orientation of the track density
>> image depends upon the -template image supplied for tracks2prob step when
>> generated. If I use the FA maps as the template, does this automatically
>> put the ROI drawn from the resultant track density maps in diffusion space?
>> If so I presume I can use these ROI to directly filter the streamlines I'm
>> interested from the whole brain tractography .tck file without applying any
>> transformation?
>>
>> Many thanks in advance
>>
>> Dan
>>
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