Reconstruction and fiber tracking with DSI-Studio on a qsipreprocessed dataset

[Johannes Wiesner]

Hi Frank, 

I just posted this question on neurostars.org:

https://neurostars.org/t/reconstruction-and-fiber-tracking-with-dsi-studio-on-a-qsipreprocessed-dataset/24037

The fundamental question is if you can run the default DSI-Studio steps (1. Getting .src files, 2. Running reconstruction, 3. Fibertracking) on qsipreprocessed data (i.e. motion-correction and eddy-current correction has already been done). Only the reconstruction and fiber tracking is still missing. I thought I could just run my bash scripts for reconstruction and fiber tracking that I used for the minimally preprocessed HCP data again on the dataset. But then Matt Cieslak said that it's 

[...] possible to use DSI Studio directly on these outputs but be careful on how the bvecs are interpreted. The version of DSI Studio in qsiprep is a bit behind the current DSI Studio and interprets bvecs differently. The bvec file is in LPS+ world coordinates, not LAS+ voxel coordinates (the FSL convention)

I actually already run:

1.) dsi_studio --action=src [...]
2.) dsi_studio --action=rec --method=7 [...]

3.) dsi_studio --action=trk [...]

--step_size=1
--turning_angle=55
--min_length=10
--max_length=400
--fiber_count=100000
--connectivity=/atlas/Glasser_TianS1.nii.gz
--connectivity_value=count,ncount,mean_length,qa,dti_fa,md,gfa,iso
--connectivity_threshold=0 [

on my files and the output doesn't look odd to me. So I wonder if DSI-Studio does take care of the different spatial axes in the background?

Greetings,

Johannes

[Fang-Cheng Yeh]

It looks good to me.

You may consider specifying --check_btable=1 with the rec command, so the b table problem will be handled.

Frank

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[Johannes Wiesner]

Ah okay, so that means --action=rec will automatically take care of this issue? :) "You may consider specifying --check_btable=1 with the rec command, so the b table problem will be handled." Which is the default anyway right? So I don't have to set this explicitly?

[Johannes Wiesner]

Ah wait...It's not 1 by default? Just checked the log files, is this a documentation bug then? Because on the homepage the default is desribed as 1:  https://dsi-studio.labsolver.org/doc/cli_t2.html

[Fang-Cheng Yeh]

Whether it is default 1 depends on the versions.
Frank

On Fri, Dec 2, 2022 at 11:59 AM Johannes Wiesner

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