modifying save_h3view_image visualisation by command line

[Xavreila Ng]

Hello Frank,

I'm trying to output two horizontal 3 view images (coloured by local index inc_t/dec_t and by assignment) using the following code in windows command prompt.

D:\my_directory>"C:\Program Files\dsi_studio_win\dsi_studio.exe" --action=vis --source=Age.t25.fdr0.05.t_statistics.fib.gz --tract=Age.t25.fdr0.05_sep_fdrcorr.dec.tt.gz --cmd="add_surface,Full+set_zoom,1+set_param,tract_color_style,{2/1}+save_h3view_image,my_image.h3view_image.jpg"

Q1. tract_color_style,2 would automatically render tracts by "qa". How can we render by dec_t/inc_t instead?

Q2. tract_color_style,1 would automatically assign "yellow" to all tracts. How can we assign other colours instead?

Thanks,
Xav

[Frank Yeh]

Currently these features are not yet available through CLI but I am
listing them on the wish list.
Frank

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[Frank Yeh]

For Q2, you may use

load_track_color,color.txt

color.txt is a text file storing the color. You may check the format
by saving the track color in the GUI.

[Xavreila Ng]

Hi Frank,

Thanks so much for the prompt reply! I've tried the solution but run into some problems.

In GUI, importing a 9-line TXT of RGB value would result in 1 colour for each of the 9 bundles (desired output), as shown below:



But with the updated command line shown below, it seems the colouring is done tube by tube and started from the last bundle in TT file, so the same TXT can only cover part of C_PHP_L which has total number of tract at 74.

D:\my_directory>"C:\Program Files\dsi_studio_win\dsi_studio.exe" --action=vis --source=t_statistics.fib.gz --tract=tracts.tt.gz --cmd="add_surface,Full+set_zoom,1+set_param,tract_color_style,2+load_track_color,colour.txt+save_h3view_image,my_image.jpg"



If I loop the RGB value until line 74, there seems to be no additional colouring. C_PHP_L remains partially coloured.

An additoinal question on GUI: after [Tracts Cluster][Sort Tracts by Name], any way to re-sort by number of tract?

Thanks,
Xav

[Frank Yeh]

I will see how I can fix this and get back to you.
Frank

On Thu, Aug 15, 2024 at 9:38 AM Xavreila Ng <xav.n...@gmail.com> wrote:
>
> Hi Frank,
>
> Thanks so much for the prompt reply! I've tried the solution but run into some problems.
>
> In GUI, importing a 9-line TXT of RGB value would result in 1 colour for each of the 9 bundles (desired output), as shown below:
>
>
>

> But with the updated command line shown below, it seems the colouring is done tube by tube and started from the last bundle in TT file, so the same TXT can only cover part of C_PHP_L which has total number of tract at 74.
>
> D:\my_directory>"C:\Program Files\dsi_studio_win\dsi_studio.exe" --action=vis --source=t_statistics.fib.gz --tract=tracts.tt.gz --cmd="add_surface,Full+set_zoom,1+set_param,tract_color_style,2+load_track_color,colour.txt+save_h3view_image,my_image.jpg"
>
>
>

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/c032e8af-cbd4-4cc6-88ed-a36a243930f3n%40googlegroups.com.

[Frank Yeh]

I checked the code and found the solution. You may need to specify the
cluster index to assign color to other tracts:

try adding an additional index like this
load_track_color,colour0.txt,0
load_track_color,colour1.txt,1
load_track_color,colour2.txt,2
...

[Xavreila Ng]

Hi Frank,

Not sure if I've misunderstood the solution since my output images are off.

I tried calling the 9-line TXT (colour.txt) which would colour a few tracts in each bundle,

"C:\Program Files\dsi_studio_win\dsi_studio.exe" --action=vis --source=t_statistics.fib.gz --tract=tracts.tt.gz --cmd="add_surface,Full+set_zoom,1+set_param,tract_color_style,2+

load_track_color,colour.txt,0+

load_track_color,colour.txt,1+

load_track_color,colour.txt,2+

load_track_color,colour.txt,3+

load_track_color,colour.txt,4+

load_track_color,colour.txt,5+

load_track_color,colour.txt,6+

load_track_color,colour.txt,7+

load_track_color,colour.txt,8+save_h3view_image,testing4.jpg"

and calling the RGB values line by line stored in 9 TXT (colour{0...8}.txt) would colour even less tracts.
(ditto)

load_track_color,colour0.txt,0+

load_track_color,colour1.txt,1+

load_track_color,colour2.txt,2+

load_track_color,colour3.txt,3+

load_track_color,colour4.txt,4+

load_track_color,colour5.txt,5+

load_track_color,colour6.txt,6+

load_track_color,colour7.txt,7+

load_track_color,colour8.txt,8+save_h3view_image,testing5.jpg"