GUI vs Command Line

[maedeh khalilian]

Dear Frank

I use the same tract file, the same atlas(i.e. AAL2) and the same parameters (end region, count ) and the same threshold to calculate connectivity matrix for a specific subject using GUI and command line, but my connectivity matrices and the graph parameters get a little different.

I wonder why it is like this.

I would be grateful if you could help me with it.

Best regards

Maedeh

[Frank Yeh]

You may check the parameter ID reported in the text report to see if
any of the settings is different.
If there are random parameters used in fiber tracking, e.g. then there
could be differences due to randomization.
Best,
Frank

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[maedeh khalilian]

Yes, there are. But I use exactly the same tract file...I mean for calculating by GUI I load the same tract file that I use in the command line...

On 19 Jan 2021 18:15, "Frank Yeh" <fran...@gmail.com> wrote:

You may check the parameter ID reported in the text report to see if
any of the settings is different.
If there are random parameters used in fiber tracking, e.g. then there
could be differences due to randomization.
Best,
Frank

On Tue, Jan 19, 2021 at 12:10 PM maedeh khalilian <maede...@gmail.com> wrote:
>
> Dear Frank
> I use the same tract file, the same atlas(i.e. AAL2) and the same parameters (end region, count ) and the same threshold to calculate connectivity matrix for a specific subject using GUI and command line, but my connectivity matrices and the graph parameters get a little different.
> I wonder why it is like this.
> I would be grateful if you could help me with it.
> Best regards
> Maedeh
>
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[maedeh khalilian]

I drop boxed you a zip file(Test_maedehKhalilian.zip) including my fib file, tract file, .bat and log.txt if they are needed to check the results...

Thanks more

On Tuesday, January 19, 2021 at 6:15:19 PM UTC+1, Frank Yeh wrote:

You may check the parameter ID reported in the text report to see if
any of the settings is different.
If there are random parameters used in fiber tracking, e.g. then there
could be differences due to randomization.
Best,
Frank

On Tue, Jan 19, 2021 at 12:10 PM maedeh khalilian <maede...@gmail.com> wrote:
>
> Dear Frank
> I use the same tract file, the same atlas(i.e. AAL2) and the same parameters (end region, count ) and the same threshold to calculate connectivity matrix for a specific subject using GUI and command line, but my connectivity matrices and the graph parameters get a little different.
> I wonder why it is like this.
> I would be grateful if you could help me with it.
> Best regards
> Maedeh
>
> --
> 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-s...@googlegroups.com.

[Frank Yeh]

I found the cause of the problem.

The *.tt.gz format is a lossy format, and the track coordinates will have a resolution at 1/32 of the voxel size. Therefore, the original tract and the one loaded from tt.gz will have a tiny difference, and that difference may affect the connectivity a bit.

If you save the files as *.trk.gz, then the matrix value will be the same.

Best,

Frank

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[maedeh khalilian]

Thank you dear Frank

Actually, I made some changes and finally I could get the same output by using tt.gz.

However, I am trying by saving the tract file as .trk.gz. The size of the .tt.gz is about 100MB but the size of the trk.gz is about 900MB.

What is the reason of this big difference?

best

Maedeh

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[Frank Yeh]

You can think of trk as a BMP file, and tt a JPG file.
tt is a lossy format and has a resolution limit of 1/32 voxel size.
Thus any coordinates will be round to this resolution limit.

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