Hi Todd<br><br>Glad to hear you'll be acquiring the reversed phase-encode data for your new project.<br><br>I had hoped to create a pulse sequence for this purpose and distribute it; unfortunately I'm still having trouble wrapping my head around the Siemens image reconstruction back-end, so I don't have it working yet. In the meantime, I can walk you through the steps we took ourselves to get the protocols required for this acquisition; this should hopefully work for anybody using a Siemens scanner.<br>
<ul><li>Make a copy of your DWI sequence protocol, and open the copy in the protocol editor.</li><li>In the 'diffusion' tab, reduce the number of diffusion weightings to 1; this should leave just a b=0 acquisition. The acquisition time for the new protocol should be around 3 TR's (a couple to reach steady-state, and one to acquire). Give this protocol a meaningful name e.g. "DWI RevPE A>>P".<br>
</li><li>Make another copy of the protocol you just created, and change the relevant part of the protocol name to "P>>A".</li><li>In the second new protocol, go to the 'routine' tab (may be in 'program'? I'm going from memory here). It should show the phase encode direction as "A>>P" (assuming this is how you acquire your DWIs; it's most common). The relevant drop-down menu will only give you the options of "A>>P" and "L>>R"; however there's a little button with "..." on it hidden next to the drop-down menu. Click on this button, and a new window will appear that allows you to rotate the phase encode direction. Slide the bar to 180 degrees and click OK, and the protocol editor should now show the phase encode direction as "P>>A".</li>
</ul>In our lab we acquire two of these images - A>>P and P>>A - before running the DWI sequence. Technically if you acquire a b=0 in your DWI sequence you only need the P>>A (as you can extract an A>>P image from the acquired DWIs), but it makes things simpler and clearer if you acquire both explicitly.<br>
<br>Happy distortion correction<br>Rob<br><div><br>--<br><br>Robert Smith<br>PhD Candidate <br><br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>245 Burgundy Street<br>
Heidelberg Vic 3084<br>Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span></div>
<br><br><div class="gmail_quote">On Mon, Mar 11, 2013 at 4:27 PM, Todd Jolly <span dir="ltr"><<a href="mailto:todd.jolly@uon.edu.au" target="_blank">todd.jolly@uon.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p>Hi Rob,</p>
<p>Our lab is about to start a new project and we are setting up our MRI protocol. I asked the radiographer about acquiring a reverse-phased encoded b0<a></a> pair to correct for the susceptibility distortions and he said to me that he doesn't know how to change
the polarity of the TSE EPI<a></a> sequence? I was wondering, if possible, would you be able to send me a dicom<a></a> image data file or an edx<a></a> file of the sequence you used so that he can figure out how you acquired the reverse-phased b0<a></a> pair?
or MR images will be acquired using a 3T<a></a> Siemens Skyra<a></a>.</p>
<p> </p>
<p>Thanks in advance</p>
<p>Todd</p>
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<div style="DIRECTION:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Todd Jolly<br>
<b>Sent:</b> Monday, 14 January 2013 2:04 PM<br>
<b>To:</b> Robert Smith; mrtrix mailinglist<br>
<b>Subject:</b> RE: [Mrtrix-discussion] TDI map differs from FA map<br>
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Hi Rob,<br>
I have read through your SIFT paper and, if possible, I would very much like to employ your SIFT method of filtering the tractogram.<br>
I'm still a little unsure of a few things. Firstly, does the filtering algorithm require the white matter partial volume mask or is the mask just used for seeding tractography? Also is the FOD segmentation based on the CSD of the diffusion-images?<br>
<br>
Unfortunately I have finished testing and didn't acquire a reversed-phase-encode b=0 pair so I are unable to correct for susceptibility distortions. Will this be likely to cause problems in performing the SIFT procedure? Would non-linearly registering the T1
to the diffusion-weighted image help increase correspondence between the T1 and FA map in my case?<br>
<br>
Thank you again for all your help<br>
Todd<br>
<div style="font-size:16px;font-family:Times New Roman">
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<div style="DIRECTION:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Robert Smith [<a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a>]<br>
<b>Sent:</b> Sunday, 6 January 2013 12:22 PM<br>
<b>To:</b> Todd Jolly; mrtrix mailinglist<br>
<b>Subject:</b> Re: [Mrtrix-discussion] TDI map differs from FA map<br>
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<div>Todd<br>
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<div>The pattern you are seeing there is fairly typical. There is streamline density throughout the genu, but it's much higher at the inferior / posterior edge.</div>
<div>The streamline density at any given point is influenced by more than just the FOD amplitude: how the streamlines are seeded, the length of the pathway(s) involved, curvature, and any biases present in the tracking algorithm (which are hard to quantify).
In this case, the increased density at the inferior / posterior edge is probably caused by having a greater number of streamlines entering that part of the genu, more so than the tracking within the genu itself (where curvature overshoot may play a small role).</div>
<div>These are precisely the sort of unwanted influences that my SIFT method aims to remove.</div>
<div><br>
</div>
<div>Rob</div>
<div class="gmail_extra"><br clear="all">
<div><br>
--<br>
<br>
Robert Smith<br>
PhD Candidate <br>
<br>
The Florey Institute of Neuroscience and Mental Health<br>
Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>
Heidelberg Vic 3084<br>
Ph: <a href="tel:%2B61%203%209035%207128" value="+61390357128" target="_blank">+61 3 9035 7128</a><br>
Fax: <a href="tel:%2B61%203%209035%207301" value="+61390357301" target="_blank">+61 3 9035 7301</a><br>
<a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br>
<span style="FONT-FAMILY:'Times New Roman','serif';COLOR:red;FONT-SIZE:9pt"></span></div>
<br>
<br>
<div class="gmail_quote">On Sun, Jan 6, 2013 at 5:11 AM, Todd Jolly <span dir="ltr">
<<a href="mailto:todd.jolly@uon.edu.au" target="_blank">todd.jolly@uon.edu.au</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
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<div style="FONT-FAMILY:Tahoma;DIRECTION:ltr;FONT-SIZE:10pt">Hi Robert,<br>
Thanks for that information, I think the anatomically constrained approach that you are working on is great and should increase accuracy/confidence of white matter classification.
<br>
<br>
In regard to the difference between my TDI and FA images, Im not sure if the previous images accurately depicted my problem. I have attached 3 more images that show CSD orientation plot, TDI colour image and the result from streamtrack (SD_PROB). I have noticed
that the streamlines do not follow the orientation of the csd dumbbells. I understand that the susceptibility induced geometric distortions you mentioned before would cause a difference between epi and anatomical images. But I didn't think these distortions
would cause there to be errors in the streamtrack accuracy when overlayed onto the CSD image, as this is based on the epi data?<br>
<br>
I have seen this mentioned before and it was due to a problem with the streamtrack program, but has since been corrected. I am using the version 0.2.10 for Linux 64 bit.
<br>
<br>
Thanks again for all your help<br>
Todd<br>
<br>
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<div style="DIRECTION:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Robert Smith [<a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a>]<br>
<b>Sent:</b> Saturday, 5 January 2013 10:42 PM<br>
<b>To:</b> Todd Jolly; mrtrix mailinglist
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<div><br>
<b>Subject:</b> Re: [Mrtrix-discussion] TDI map differs from FA map<br>
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<div>Todd<br>
<br>
Thanks for sending those images; it makes the discussion a whole lot more clear.<br>
<br>
Firstly, I don't see anything fundamentally 'wrong' with your images; your processing appears to be fine.<br>
I would however like to discuss a few points with regards to the observations you have made, for anyone interested enough to continue reading:<br>
<br>
<br>
* Although you haven't provided an example image, you noted that the discrepancy between the TDI and anatomical image appears most prominent in the genu of the corpus callosum.<br>
Most likely this is caused by susceptibility-induced geometric distortions. For a standard EPI acquisition with the phase-encode direction running anterior-posterior, the genu is shifted posteriorly by as much as a couple of voxels; it's not enough
to make the DWIs look 'wrong' when viewed independently, but it's highly noticeable when you overlay them on a non-EPI image.<br>
In my experience, the best results for susceptibility distortion correction (in terms of both acquisition time and accuracy) are obtained using the reversed-phase-encode method (<a href="http://www.sciencedirect.com/science/article/pii/S1053811909012294" target="_blank">this</a><a>
method</a> is probably easiest to read and understand). Our lab now acquires a reversed-phase-encode b=0 pair for this purpose, for every subject scanned. I had done some experimentation with methods for estimating the inhomogeneity field from such an image
pair, in the hope of including something in MRtrix, but the tools included in FSL5 ('topup' and 'applytopup') work better than anything I've come up with thus far. You do NOT need to acquire a reversed phase-encode image for every single DW direction (although
it can yield better results); a single echo-planar image pair is enough to estimate the inhomogeneity field and 'shift' the DW signal back to its correct spatial position.<br>
<br>
* The overlap between the TDI and the ventricles is commonplace, and occurs due to a combination of factors.<br>
The default FOD amplitude threshold for streamline termination is 0.1; maximal FOD values are around 3.0. Now imagine a voxel that is half corpus callosum, half ventricle, that has an FOD peak amplitude of 1.5, and the voxel adjacent to it is in the
ventricle and has zero FOD amplitude. As the streamlines algorithm interpolates the FODs as it tracks, streamlines can go almost all the way out to the centre of the ventricle voxel before the (interpolated) FOD amplitude threshold is disobeyed; this is why
the tracking algorithm substantially over-estimates the cgrant batemanross-section of the corpus callosum (clearer when viewed on a mid-sagittal slice of the T1 / TDI).<br>
Correction of reconstruction errors such as this are the target of my <a href="http://www.sciencedirect.com/science/article/pii/S1053811912005824" target="_blank">
Anatomically-Constrained Tractography</a> framework, which makes use of a segmented T1 image during the tracking process. Streamlines entering the ventricles are not only terminated, but rejected entirely (as we don't expect white matter connections to enter
the ventricles). This will be included in the next major release of MRtrix; but it relies on very good correspondence between the DWIs and the T1, which is why I recommend acquisition of reversed-phase-encode image pairs as soon as possible (so you can use
this capability on retrospective data).<br>
<br>
* The final issue you raise is the contrast present in the TDIs, where the intensity is highest in the corpus callosum (particularly its inferior edge) and doesn't necessarily match the FA map.<br>
This is not surprising at all, as the two images draw their contrast from very different sources. Neither the streamline density nor the FA are accurate markers of 'white matter connection density' (<a href="http://www.sciencedirect.com/science/article/pii/S1053811912007306" target="_blank">this
paper</a> by Derek Jones is worth a read), so care needs to be taken in the interpretation of both sources.<br>
But since I've already strayed down the path of self-proclamation, I might as well mention my recently-published
<a href="http://www.sciencedirect.com/science/article/pii/S1053811912011615" target="_blank">
SIFT</a> method. This tries to match the streamline densities with the tissue volumes estimated by CSD; as a result, the TDIs look very much like the DC term of the relevant FOD image. To me this is a much better quantification of 'white matter connection density'
than FA, TDI, or the <i>ad hoc</i> metrics being used by the connectomics community. So I'm looking forward to seeing what people do with it when it's released.<br>
<br>
<br>
<br>
Anyway, I hope that was all at least somewhat interesting / informative for yourself or others out there in the ęther...<br>
<br>
Rob<br clear="all">
<div class="gmail_extra">
<div><br>
--<br>
<br>
Robert Smith<br>
PhD Candidate <br>
<br>
The Florey Institute of Neuroscience and Mental Health<br>
Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>
Heidelberg Vic 3084<br>
Ph: <a href="tel:%2B61%203%209035%207128" value="+61390357128" target="_blank">+61 3 9035 7128</a><br>
Fax: <a href="tel:%2B61%203%209035%207301" value="+61390357301" target="_blank">+61 3 9035 7301</a><br>
<a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br>
<span style="FONT-FAMILY:'Times New Roman','serif';COLOR:red;FONT-SIZE:9pt"></span></div>
<br>
<br>
<div class="gmail_quote">On Sat, Jan 5, 2013 at 7:31 PM, Todd Jolly <span dir="ltr">
<<a href="mailto:todd.jolly@uon.edu.au" target="_blank">todd.jolly@uon.edu.au</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:rgb(204,204,204) 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>
<div style="FONT-FAMILY:Tahoma;DIRECTION:ltr;FONT-SIZE:10pt">Hi Rob,<br>
No problem, I have attached a couple of images to show you what I mean. These show the TDI overlayed on the FA map.<br>
Thanks<br>
Todd<br>
<div style="FONT-FAMILY:Times New Roman;FONT-SIZE:16px">
<hr>
<div style="DIRECTION:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Robert Smith [<a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a>]<br>
<b>Sent:</b> Saturday, 5 January 2013 2:13 PM<br>
<b>To:</b> Todd Jolly<br>
<b>Subject:</b> Re: [Mrtrix-discussion] TDI map differs from FA map<br>
</font><br>
</div>
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<div></div>
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<div>Todd<br>
</div>
<div><br>
</div>
<div>Could you forward me a couple of example images to demonstrate exactly what you mean? It's difficult to establish what the problem may be from your description alone.</div>
<div><br>
</div>
<div>Rob</div>
<div class="gmail_extra"><br clear="all">
<div><br>
--<br>
<br>
Robert Smith<br>
PhD Candidate <br>
<br>
The Florey Institute of Neuroscience and Mental Health<br>
Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>
Heidelberg Vic 3084<br>
Ph: <a href="tel:%2B61%203%209035%207128" value="+61390357128" target="_blank">+61 3 9035 7128</a><br>
Fax: <a href="tel:%2B61%203%209035%207301" value="+61390357301" target="_blank">+61 3 9035 7301</a><br>
<a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br>
<span style="FONT-FAMILY:'Times New Roman','serif';COLOR:red;FONT-SIZE:9pt"></span></div>
<br>
<br>
<div class="gmail_quote">On Sat, Jan 5, 2013 at 1:57 PM, Todd Jolly <span dir="ltr">
<<a href="mailto:todd.jolly@uon.edu.au" target="_blank">todd.jolly@uon.edu.au</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:rgb(204,204,204) 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>
<div style="FONT-FAMILY:Tahoma;DIRECTION:ltr;FONT-SIZE:10pt">Hi everyone,<br>
I have been performing whole-brain tracking and using this to generate track density images. I have noticed that the track density images differ from my anatomical or FA images. The TDI appear to be including regions that the anatomical images are classifying
as being the lateral ventricle. This is most noticeable for the genu of the corpus callosum.<br>
I am concerned as these regions that are classified as CSF in the anatomical and FA images appear have the highest track density in the TDI? Is this normal for there to be a discrepancy or have I made an error somewhere in the processing of these data?<br>
Thanks in advance<span><font color="#888888"><br>
Todd<br>
</font></span></div>
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