A Problem with Exporting TDI in Command Line

[maede...@gmail.com]

Dear Frank

I run a command line like :

  --action=trk --source=...fib.gz  --fiber_count=1000000 --thread_count=12 --turning_angle=45 --step_size=0.75 --min_length=30 --max_length=300  --fa_threshold=0.00 --otsu_threshold=0.6  --tip_iteration=2 --export=tdi2 --output=..fib.gz.trk.gz" > "${f}.log.txt"

 to do a tractography for a specific subject.

Then I run the command line 

 --action=ana  --source=...fib.gz  --tract=...fib.gz.trk.gz   --t1t2=${L}.t1.nii  --roa=${L}  --export=tdi2  --output="$f".$L.filtered.trk.gz  >  "${f}.filtered.log.txt"

 inorder to filter out the tracks by a lesion.

Now my problem is that the tract density image I get before and after filtering are not in the same space. While when i do all these processes via gui, the both nifti files are in the same space.

the both density nifti files (outputs of the first and the second commandl ines)are attached in case u want to check them.

I would be grateful if you could help me find a solution.

let me know if u need to check the outputs I got from GUI as well.

Best regards

Maedeh;  

[maede...@gmail.com]

The  nifti file before filtering is of big size. I will dropbox it...

Best,

Maedeh

[Frank Yeh]

You may try --export=tdi and it will output in the same space.
Frank

> --
> You received this message because you are subscribed to the Google Groups "DSI Studio" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/58ca5e02-cc3a-4fd0-80a9-cb424e2ce833n%40googlegroups.com.

[maede...@gmail.com]

Dear frank 

This is what I get from --export=tdi.

still not in the same space

Maedeh

[Frank Yeh]

Could you post the log output of these two commands?
Frank

On Tue, Oct 5, 2021 at 10:16 AM maede...@gmail.com

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/e0b1ecd1-8e5c-4ee1-b893-316963b8550bn%40googlegroups.com.

[maede...@gmail.com]

yes Sure.

This is for another subject.

But the same problem

[Frank Yeh]

Thank you very much.
I am fixing the bug.

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/407b216e-e9e3-426f-a1ff-610d1d60c295n%40googlegroups.com.

[Frank Yeh]

Here's the updated version:
https://www.dropbox.com/s/m1f8cr6our0ql35/dsi_studio_64.zip?dl=0
Please see if it works for you.
Best regards,
Frank

[maedeh khalilian]

Thank you very much.I  look forward to it...

> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+unsubscribe@googlegroups.com.

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/407b216e-e9e3-426f-a1ff-610d1d60c295n%40googlegroups.com.

--
You received this message because you are subscribed to the Google Groups "DSI Studio" group.

To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtL432HkTvR_5QNBentdxUQzJKL1j4g4CRKjFOQdZRQfAw%40mail.gmail.com.

[maede...@gmail.com]

Thank you very much dear Frank.

I will test and let you know. But, actually in this new version there are some changes for example the folder of templates doesnt exist anymore and I can not write the name of my own atlas in  "HCP1065.QA.nii.gz.atlas.txt" and in conclusion I can not use my own atlas for calculating connectivity matrices via commanline.

So I prefere to use the previous version.

I will drop box the version I am currently use.

I wonder if it is possible to fix the bug in this version so I don need to  use another version.

[maede...@gmail.com]

Dear Frank 

In the new version I dont get any outputs for TDI,,,,I tried --export=tdi2,,,3

The log files are attached...

[Frank Yeh]

The problem is the --t1t2 option, and DSI Studio thought you would
like to have TDI in the t1t2 space.
A solution is to use ROA in the native space and remove the t1t2 option.

The new version has all templates in the /atlas/ICBM152 folder.
The files only have location changes.

Best,
Frank

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/a4af520d-1e24-49e4-82c3-2059da330111n%40googlegroups.com.

[maede...@gmail.com]

Aw, Yes You are right.

Thank you very much.

I changed the structure of coding and now it works.

So sorry for asking many questions...

The resolution of the tdi I get in commandline is 2mm. How can I  increase the resolution to 1mm?

Because when I do it by GUI the resolution is 1mm.

[maedeh khalilian]

Dear Frank
I did it by using tdi2.
It is solved.
Thanks millionss s...

You received this message because you are subscribed to a topic in the Google Groups "DSI Studio" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/dsi-studio/XCL1Rk1ztFs/unsubscribe.
To unsubscribe from this group and all its topics, send an email to dsi-studio+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/b044334f-266c-4198-a171-52a6cf7edceen%40googlegroups.com.