# Finding tracks between ROIs: tckedit on WB tractogram or targeted tracking

**URL:** https://community.mrtrix.org/t/finding-tracks-between-rois-tckedit-on-wb-tractogram-or-targeted-tracking/2203
**Category:** Uncategorized
**Tags:** tractography
**Created:** [January 23, 2019, 10:33pm UTC](https://community.mrtrix.org/t/finding-tracks-between-rois-tckedit-on-wb-tractogram-or-targeted-tracking/2203 "2019-01-23T22:33:26Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![Xiaoxiao\_Qi](https://community.mrtrix.org/user_avatar/community.mrtrix.org/xiaoxiao_qi/32/2193_2.png) [@Xiaoxiao\_Qi](https://community.mrtrix.org/u/Xiaoxiao_Qi)
#### Post date: [January 23, 2019, 10:33pm UTC](https://community.mrtrix.org/t/finding-tracks-between-rois-tckedit-on-wb-tractogram-or-targeted-tracking/2203/1 "2019-01-23T22:33:26Z")

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Dear MRtrix experts,

I am trying to find a method to extract tracks starting from one gray matter region, traversing a white matter ROI, to another gray matter region.

I’ve read a few posts related to this question, but it seems there is no one best way to do it.

Basically, I’ve read about three ways to do this:

1. do whole brain tractography with dynamic seeding; then do SIFT; then do tckedit with include regions. ([Finding tracts from one region to another region](https://community.mrtrix.org/t/finding-tracts-from-one-region-to-another-region/1196))
2. use tckgen to do targeted tractography with ROI induced constraints. ([Tckedit or tckgen for tract dissection](https://community.mrtrix.org/t/tckedit-or-tckgen-for-tract-dissection/1654))
3. Merge targeted tracking pathways with whole brain tractogram; then do SIFT; then do tckedit with include regions. ([Tckedit after targeted tracking](https://community.mrtrix.org/t/tckedit-after-targeted-tracking/1835))

I am wondering what are the differences among these methods, especially between method 1 and method 3 and which one I should use in my case.

Sorry if my questions are too basic and thank you in advance for your kind help!

Best,  
Xiaoxiao

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### Author: ![rsmith](https://community.mrtrix.org/user_avatar/community.mrtrix.org/rsmith/32/2672_2.png) [@rsmith](https://community.mrtrix.org/u/rsmith)
#### Post date: [January 27, 2019, 12:34pm UTC](https://community.mrtrix.org/t/finding-tracks-between-rois-tckedit-on-wb-tractogram-or-targeted-tracking/2203/2 "2019-01-27T12:34:42Z")

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So there’s a couple of different points to consider here: one is in the _selection_ of streamlines, the other is the _quantification_ of connection strength.

For selection of streamlines corresponding to a bundle, I tend to recommend the `tck2connectome` - `connectome2tck` approach that’s been described in other threads, as it’s more likely to result in the “expected” behaviour when selecting streamlines based on grey matter regions of interest (where ACT-terminated streamlines may not actually intersect a ROI if it is defined only inside grey matter voxels).

For quantification, only 1 and 3 permit quantitative interpretation of connectivity using the SIFT model. Though note that 3 only works with SIFT2: SIFT would simply remove the large number of streamlines within your pathway of interest as part of its optimisation process. If your pathway is reasonably large, I would suggest sticking with approach 1 for simplicity.

Rob

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### Author: ![Xiaoxiao\_Qi](https://community.mrtrix.org/user_avatar/community.mrtrix.org/xiaoxiao_qi/32/2193_2.png) [@Xiaoxiao\_Qi](https://community.mrtrix.org/u/Xiaoxiao_Qi)
#### Post date: [January 29, 2019, 12:55am UTC](https://community.mrtrix.org/t/finding-tracks-between-rois-tckedit-on-wb-tractogram-or-targeted-tracking/2203/3 "2019-01-29T00:55:21Z")

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Dear Rob,

Thank you for you kind reply.

Xiaoxiao