# Streamlines tractography output problem

**URL:** <https://community.mrtrix.org/t/streamlines-tractography-output-problem/903>\
**Category:** Uncategorized\
**Created:** [May 17, 2017, 9:51pm UTC](https://community.mrtrix.org/t/streamlines-tractography-output-problem/903 "2017-05-17T21:51:34Z")\
**Posts on this page:** 1\
**Showing post:** 8

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**Author:** ![SuperClear](https://community.mrtrix.org/user_avatar/community.mrtrix.org/superclear/32/2222_2.png) [@SuperClear](https://community.mrtrix.org/u/SuperClear)\
**Post date:** [November 8, 2017, 9:04pm UTC](https://community.mrtrix.org/t/streamlines-tractography-output-problem/903/8 "2017-11-08T21:04:30Z")

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Hi, Donald,

I mainly test ACT method on two data sets, and what I concerned most are the following two points:

1. The corpus callosum fibers are incomplete, as shown in Fig.1-5 and Fig 2-5.
2. The tckgen results a lot of short fibers, as shown in Fig 1-4.

I also had tried:  
A) increase fiber number: up to 1M;  
B) Change mask: white matter mask → whole brain mask.  
C) seeding mechanisms: `-seed_dynamic` and `-seed_gmwmi`

But the comeout has no any improvement.  
Can you provide me some suggestion?

Thanks,  
Chaoqing

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**1. ACT with data1**

I register DTI and T1 to MNI152 space as [Lucius](http://community.mrtrix.org/t/registration-of-structural-and-diffusion-weighted-data/203/22) suggested.

Fig. 1-0. ( mrview: T1, DTI, WM, GMWMI in MNI152 space)

 ![gmwmi](https://community.mrtrix.org/uploads/default/original/1X/de6f29041b81e9206053fcb2f561c66c35e4e810.jpg)

Fig. 1-1. ( response function )

 ![DTI_2013_freesurfer_in_MNI152_wmsegMNI152_response](https://community.mrtrix.org/uploads/default/original/1X/df61b429df299e02da8a463112a7701a174a3582.png)

Fig. 1-2. (white matter mask)

 ![seg_in_MNI152](https://community.mrtrix.org/uploads/default/original/1X/09bb165afd8d4ddc310adb7a6f8ea71c176034af.jpg)

Fig. 1-3. (Fiber orientation distribution)

 ![png](https://community.mrtrix.org/uploads/default/original/1X/3f28be7c12e0a87fdd30489124930c6011baa702.jpg)

Fig. 1-4. (tckgen -act result)

 ![DTI_2013_ freesurfer_in_MNI152_wmsegMNI152_act_gmwmi_backtrack_1M_01](https://community.mrtrix.org/uploads/default/original/1X/badabc411497e4d90ee45155b305b27a6de45a78.png)

Fig. 1-5. (The rendering result)

 ![1M](https://community.mrtrix.org/uploads/default/original/1X/c14390b2f5bd852c6e729f4fbb597199ed631f26.png)

[ACT commands]:

> 1. 5ttgen fsl t1\_2013\_freesufer\_in\_MNI152.nii.gz t1\_2013\_freesufer\_in\_MNI152\_nocrop\_5TT.nii.gz -nocrop
> 
> 2. 5tt2gmwmi t1\_2013\_freesufer\_in\_MNI152\_nocrop\_5TT.nii.gz t1\_2013\_freesufe  
> r\_in\_MNI152\_nocrop\_5TT\_gmwmi.mif
> 
> 3. dwi2response tournier DTI\_2013\_freesurfer\_in\_MNI152.nii.gz DTI\_2013\_free  
> surfer\_in\_MNI152\_fswm\_response.txt -mask t1\_2013\_freesufer\_wm\_in\_MNI152.nii.gz -fslgrad DTI\_2013.bvecs DTI\_2013.bvals
> 
> 4. dwi2fod csd DTI\_2013\_freesurfer\_in\_MNI152.nii.gz DTI\_2013\_freesurfer\_in\_  
> MNI152\_fswm\_response.txt DTI\_2013\_freesurfer\_in\_MNI152\_fswm\_fod.mif -mask t1\_2013\_freesufer\_wm\_in\_MNI152.nii.gz -fslgrad DTI\_2013.bvecs DTI\_2013.bvals
> 
> 5. tckgen -act t1\_2013\_freesufer\_in\_MNI152\_nocrop\_5TT.nii.gz DTI\_2013\_free  
> surfer\_in\_MNI152\_fswm\_fod.mif DTI\_2013\_freesurfer\_in\_MNI152\_fswm\_act\_gmwmi\_backtrack\_0.1M.tck -crop\_at\_gmwmi -seed\_gmwmi t1\_2013\_freesufer\_wm\_in\_MNI152.nii.gz -backtrack -select 100000

* * *

**2. ACT with data2(An example data)**

Fig. 2-0 ( mrview: T1, DTI, WM, GMWMI )

 ![gmwmi](https://community.mrtrix.org/uploads/default/original/1X/d6d59d8ba816fdc604f44deb4aa957df22389ed1.jpg)

Fig. 2-1. ( response function )  
 ![HARDI150_response](https://community.mrtrix.org/uploads/default/original/1X/e6ef3bc8d904d86df48e8a58e5cdc0f82445c0f8.jpg)

Fig. 2-3. (Fiber orientation distribution)

 ![HARDI150_mrtrix_WMmask_fod](https://community.mrtrix.org/uploads/default/original/1X/1c9b5754288bcae4d4f50cb7e2080d12c5b59aef.png)

Fig. 2-4. (tckgen -act result)

 ![1M_backtrck_seeddynamic](https://community.mrtrix.org/uploads/default/original/1X/5be4d63d0c6153c34f86c20d48adbee74f6f6dc1.jpg)

Fig. 2-5. (The rendering result)

 ![HARDI150_WMvolume_act_10M_backtrck_01](https://community.mrtrix.org/uploads/default/original/1X/9aa26cab348f00c2a2b71e3e73176661bef3f72e.jpg)

[ACT commands]:

> 1. 5ttgen fsl T1\_HARDI150.nii.gz T1\_HARDI150\_5TT\_nocrop.mif -nocrop
> 
> 2. dwi2response tournier -fslgrad HARDI150.bvec HARDI150.bval HARDI150.nii.gz HARDI150\_response.txt
> 
> 3. dwi2fod csd HARDI150.nii.gz HARDI150\_response.txt HARDI150\_WMvolume\_fod.mif -mask T1\_HARDI150\_5TT\_nocrop\_WMvolume\_3D\_HARDItemplate.nii.gz -fslgrad HARDI150.bvec HARDI150.bval
> 
> 4. 5tt2gmwmi T1\_HARDI150\_5TT\_nocrop.mif T1\_HARDI150\_5TT\_nocrop\_gmwmi.mif
> 
> 5. tckgen -act T1\_HARDI150\_5TT\_nocrop.mif HARDI150\_WMvolume\_fod.mif HARDI150\_Wmvolume\_act\_0.1M\_backtrck.tck -crop\_at\_gmwmi -seed\_gmwmi T1\_HARDI150\_5TT\_nocrop\_gmwmi.mif -backtrack -select 100000

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