A Question regarding adding a new atlas

[najme soleimani]

Dear Frank,

Firstly Thanks for developing such a great software...

secondly, I want to run a bash script in order to compute connectivity matrix. I wonder how I can add my parcellations as an atlas to the DSI studio as a means to this end.

I read this link: http://dsi-studio.labsolver.org/Manual/Fiber-Tracking#TOC-Add-a-new-atlas

but the problem I encounter is that my parcellations are in T1 space of each subject (I mean for instance the parcellation of subject 1 is in T1 space of this subject) as there are the results of FreeSurfer parcellations. they are compeletly subjective.

Can registering one of the parcellation to the MNI space and then add it to the DSI studio as a new atlas be a solution?

I would be grateful if you could help me how I can add them as an atlas to DSI studio.

Thank you in advance...

Best regards,

Najme

[Frank Yeh]

You can add the original t1w as a reference by --t1t2=subject.t1w.nii.gz

When output the connectivity matrix assign the subject's parcellation using --connectivity=subject_parcellation.nii.gz

DSI Studio will check if the parcellation file has the same dimension as the subject's t1w and transform accordingly.

Best regards,

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/09b7f20e-90fe-48ee-a6aa-0ff878f2c5d0n%40googlegroups.com.

[Michel Audette]

Dear DSI Studio users, 

I would like to be able to load a T1 and DTI image dataset as well as seed points for tractography from a coordinates file, i.e.: a script. Is there a template for doing this that I could download and adapt to my own image data? 

Thanks for your support, 

Michel Audette, Ph.D.

Associate Professor, Department of Computational Modeling and Simulation Engineering,
Graduate Program Director, Biomedical Engineering Institute,
Old Dominion University,
Norfolk, VA.

[Frank Yeh]

Are your seed points in the DTI space or T1w space?

> --
> 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/CAPxub5aksN8xiDrDvDW2But-w_zLA2frzqwFMhDNWg%2BFg98ZZg%40mail.gmail.com.

[Michel Audette]

Hi Frank, 

thanks for your reply. I don't have them yet. I'm open to either option, although I think that my medical students can better navigate with the T1. Does DSI have a mechanism for identifying them and storing them in a file?

Best wishes, 

Michel

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_Qrt%2Byy4sPtDh7MtyLrgW%3D7acu6MyScjFgwbaJrwAndd_xvQ%40mail.gmail.com.

[Frank Yeh]

If the seed points can be saved to a nifti file (either in the DTI or
T1w space), then the following command line may work.

dsi_studio --action=trk --source=subject.fib.gz --fiber_count=1000000
--output=tracks.tt.gz --seed=seed.nii.gz --t1t2=subject_t1w.nii.gz

On Thu, Jul 8, 2021 at 5:43 PM Michel Audette

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAPxub5bFnkYp%3DZAf8b5gg-vrwKgqLdPm8mUGsmg1UxX9Rg2eZQ%40mail.gmail.com.

[Michel Audette]

Hi Frank, 

thanks for your kind reply. Does DSI studio make it possible to do this? Is it possible to use it in a Slicer-like manner where seed points are entered through the user interface and are saved in a fiducial list file?   https://www.slicer.org/wiki/Modules:Fiducials-Documentation-3.6

Thanks for your continued support.

Michel

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtLYa-aUXqByTFSn8AW%3DAeUfo7V0d_c_NWcd8c2NOJ1X9w%40mail.gmail.com.

[Frank Yeh]

Using GUI, yes :
http://dsi-studio.labsolver.org/Manual/Fiber-Tracking#TOC-Manually-draw-a-region
The region can then saved as NIFTI files for CLI.
Frank

On Thu, Jul 8, 2021 at 7:22 PM Michel Audette
<japanmont...@gmail.com> wrote:
>
> Hi Frank,
>
> thanks for your kind reply. Does DSI studio make it possible to do this? Is it possible to use it in a Slicer-like manner where seed points are entered through the user interface and are saved in a fiducial list file? https://www.slicer.org/wiki/Modules:Fiducials-Documentation-3.6

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAPxub5aBGYSK2mzbYzWRJYT3t-%2BNsPiJ_SZ4V3AiND-VE5gaFg%40mail.gmail.com.

[Michel Audette]

I see that a seed point is just a type of region, in your lexicon, the way that you define it. Thanks for the clarification. 

Cheers, 

Michel

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/CAG_QrtJqX3jqVigOCMrF0oFbASQER%2Bs6x0FDGSRnoDJpTnjGUQ%40mail.gmail.com.