<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
- I loaded all 3 repeated scans by adding the folders to the Dicom<br>
Image File Folders, and all the scans loaded properly.<br>
- My guess is the next step is to realign all the images using AIR. I<br>
have a couple of questions about this.<br>
- What is the optional upper bound?<br></blockquote><div><br>AIR requires us to define a threshold to remove the background signals. Otherwise, it tries to register the noise floor too. Also, AIR is sensitive to the threshold. We usually do not use upper bound, but this is to remove the CSF signals in b0 image to make the contrast closer to DWIs. <br>
<br>Because you have 3 repeated images, I recommend you to calculate STD of the repeated scan using one of the buttons in the "DtiMapping" tab ("Mean, STD, etc"). Then click "Original-ADC-Mean-STD" button. You can find two extra rows of images; one is the average of the 3 repeated scans and the other is the STD. Usually the STD images should look like nothing but noise. If the subject moved, you can see clear anatomy due to image shift and thus a king of edge-enhanced STD images. <br>
<br>You have to monitor what AIR does using this window. If the STD images look like noise, you don't have to do AIR but because AIR smooths the images (and thus enhance SNR), you'd better do AIR for all data. Make sure that AIR don't make such a data worse. If you find mis-registration in the STD images, AIR should correct them.<br>
<br>AIR results are sensitive to threshold and also cost function. It is purely try & error. Usually once it works, you don't have to change often. My experience says, threshold tends to be high side for robust performance.<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
- Which cost function is best to use?<br>
- Should I adjust the gradients for the diffusion weighted images?<br></blockquote><div><br>I don't use this function. If the subject moves so much that this gradient correction based on image registration makes a significant impact on your data (namely, if AIR rotates the brain by 5 degree, the gradient vector also has to be rotated by 5 degree), you'd better worry so many other things about the validity of the data itself. However, it is true that some reviewers believe in this and ask you "did you do it?"<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
- Once Air finishes I have a bunch of images labeled Air-series-blah\<br>
-1, Air-series-blah\ -2, etc.<br>
- How do I save these images so I can just reload them later and not<br>
have to redo-air.<br>
- How do I get DTI studio to use these images rather than the<br>
original images for the FA calculation?<br>
- How do I tell DTIstudio to combine the images across the repeats?<br></blockquote><div><br>If you unclick "create new image after registration", you registered images overwirte you original data and subsequent calculation will be based on the registered images.<br>
<br>if you leave it checked, you get an extra dataset called "AIR_xxx". In this case, you need to save the registered "AIR_xxx" images and reload them for tensor calculation. For this, you use the "save" icon in the "Image" tab. Choose the entire data (b0 + DWIs) and save them into 1 file (if you have three repetitions, into 3 files) as "raw" format. This is so-called REC format in DtiStudio.<br>
<br>When you have 3 repeated scans and load all of them, there is no particular steps to combine them. DtiStudio uses all 3 scans to fit one tensor.<br><br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Thanks again,<br>
Darren<br>
<br>
<br>
<br>
> Hi Darren,<br>
><br>
> In a previous communication in the mailing list, I explained why we can not<br>
> use regular k-space averaging for DTI and, therefore, we average data after<br>
> magnitude calculation (we average images, not k-space data). If anybody<br>
> remembers which thread it was, I would appreciate it.<br>
><br>
> Anyway, because we first have to calculate image before averaging, there is<br>
> no point to ask scanners to do the averaging. One downside of the<br>
> averaging-by-the-scanner is, if the images are mis-registered or there are<br>
> corrupted images, we can not undo the averaging.<br>
><br>
> I believe that is why Siemens always save all images separately (without<br>
> creating an "averaged image" even if multiple averaging is specified.<br>
><br>
> Please note the difference between "repeated scans (you submitted the same<br>
> protocol twice)" and "averaged scans (you specified 2 signal averaging)"<br>
> when you use Siemens. Either way, all images are saved individually and they<br>
> are basically the same studies. However, in the former case, the "repeated<br>
> images" are stored in different directories and Siemens console can not<br>
> combine them for DTI calculation. With the latter case, the repeated images<br>
> are stored in the same directory and Siemens console can combine them to<br>
> calculate one DTI data.<br>
><br>
> Either way, when you use DtiStudio, you need to load all files at once and<br>
> DtiStudio can combine them to calculate one DTI.<br>
><br>
> Now going back to your question;<br>
><br>
> 1) You can specify the number of signal averaging in Siemens. I'm not sure<br>
> why you thought you couldn't. However, if you meant, "Siemens saved all<br>
> images separately without averaging", then you are correct.<br>
> 2) DtiStudio can read repeated scans and combine them for one DTI<br>
> calculation.<br>
><br>
> On Sun, Feb 28, 2010 at 7:54 PM, Darren Gitelman <<br>
> d-gitelman at <a href="http://northwestern.edu" target="_blank">northwestern.edu</a>> wrote:<br>
><br>
> > Hello:<br>
> ><br>
> > Is there a way to combine data across several repeats of a DTI sequence?<br>
> ><br>
> > The reason I ask is that we have a Siemens Trio scanner but are<br>
> > working with another group that has a GE scanner. On the GE scanner<br>
> > the DTI sequence allows NEX > 1 (they are getting 4), which appears to<br>
> > improve their SNR considerably. The Siemens sequences do not allow<br>
> > this, so we are repeating the DTI sequence several times, and want to<br>
> > combine the data across runs. Can this be done within DTIstudio or<br>
> > some other program? Would it be best to do this at the level of the<br>
> > DTI images or the FA maps?<br>
> ><br>
> > Thanks,<br>
> > Darren<br>
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