how_to > RE: HOW TO use the DTI template for registration
Oct 20, 2015  07:10 PM | Rowena Chin - UCL
RE: HOW TO use the DTI template for registration
Hi Konstantinos,

Thanks very much for the quick and comprehensive reply.

If I understand correctly, the steps in the PDF you suggested ('HOW-TO-extract-pairs-of-GM-labels-with-connections-through-WM-ROI') aim to identify the GM regions that are connected via a WM ROI. If one were to prefer using the JHU ICBM-81 White Matter Labels (as in FSL), would this still be possible with the 256 version (as I understand the 256 version works best with DTI-TK)? I read your reply to Marcus about this and it seems that it works with the non-256 version but because the 256 version seems to be more seamless with DTI-TK, I wonder if it can still be compatible with the ICBM-81 labels.

Originally posted by Konstantinos Arfanakis:
Hi Rowena,

You are right, our HOW-TO document describing how to spatially normalize individual DTI data to the IIT Human Brain Atlas using DTI-TK describes how to register directly to the atlas and does not cover the case where a population template is first constructed and then registered to the IIT atlas. Before answering your specific questions, let me pause here to comment on the two approaches above. I tend to prefer the approach covered by our HOW-TO document. The reasons are the following. A study-specific template is theoretically most representative of the data under study and may lead to the best spatial normalization accuracy. Based on that, some users first register to a study-specific template and then register the study-specific template to the IIT atlas. However, the accuracy of spatial normalization to a study-specific template is high only when the study-specific template is carefully constructed and of high quality. Poorly constructed study-specific templates (e.g. when small number of subjects are used, or when suboptimal template-building procedures are used) are actually not representative of the individual data under study and lead to low spatial normalization accuracy. On the other hand directly registering to a high quality standardized template like the one in the IIT atlas, is shown to perform very similar to registering to a high-quality study-specific template and then registering that to the IIT atlas, and is also consistent and fast (no need to make a study-specific template). In brief, both approaches are appropriate, but if you decide to make a study-specific template first, you need to make sure that the study-specific template you are constructing is of high quality. If you cannot achieve that for whatever reason, or you don't want to worry about it, or you want to be able to compare results across studies, then register directly to the IIT atlas as shown in our HOW-TO document.
Now, in terms of your specific questions:
1) Yes, you should be able to combine the steps you mentioned with the later steps of our HOW-TO document.
2) Yes, you can perform TBSS after you have normalized to the IIT atlas. Just read the HOW-TO use the IIT atlas in TBSS document. It walks you through the steps you'll need to follow. And once you are done with your TBSS analysis in IIT space following the steps in our HOW-TO document, you can use our white matter atlas resources to help you understand your findings. For example, if you find some significant effects somewhere in white matter, you can use the "regionstat" program to give you the list of the most probable connections going through the region with the significant effects (See HOW-TO-extract-pairs-of-GM-labels-with-connections-through-WM-ROI). It does not require any tractography and is very fast. It works by interrogating our 4D white matter atlas to extract the most probable connections through your white matter ROI.

Let me know if you have more questions.
Regards,
Konstantinos

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TitleAuthorDate
Konstantinos Arfanakis Jun 5, 2013
magan Feb 13, 2018
Konstantinos Arfanakis Feb 14, 2018
magan Feb 15, 2018
Rowena C Oct 16, 2015
Konstantinos Arfanakis Oct 16, 2015
RE: HOW TO use the DTI template for registration
Rowena Chin Oct 20, 2015
Konstantinos Arfanakis Oct 21, 2015
Rowena C Jan 19, 2016
Konstantinos Arfanakis Jan 20, 2016
Lauren Byrne Mar 31, 2015
Lauren Byrne Mar 26, 2015
Konstantinos Arfanakis Mar 30, 2015
Lauren Byrne Mar 31, 2015
Lauren Byrne Mar 31, 2015
Konstantinos Arfanakis Apr 2, 2015
Lauren Byrne Apr 10, 2015
Konstantinos Arfanakis Apr 10, 2015
Lauren Byrne Apr 14, 2015
Konstantinos Arfanakis Apr 22, 2015
Lauren Byrne May 11, 2015
Konstantinos Arfanakis May 13, 2015
Lauren Byrne May 14, 2015
Konstantinos Arfanakis May 14, 2015
Lauren Byrne May 15, 2015
Lauren Byrne May 11, 2015
Lauren Byrne Apr 24, 2015
Marcus heldmann May 27, 2014
Konstantinos Arfanakis May 28, 2014
Konstantinos Arfanakis Aug 10, 2013
Sean Hatton Jan 1, 2014
Konstantinos Arfanakis Jan 3, 2014