Save trk as nii file?

[j.cos...@jatneurolab.com]

Is it possible to save a trk file as nii that is registered correctly? I can save the tract as a nii.gz extension, however the location information is all off.

Alternatively, does anyone know a way to convert trk files to nii files?

- Jamie

[j.cos...@jatneurolab.com]

Found a previous post, will try and come back.

[Fang-Cheng Yeh]

You can export track density image using [Tract][Save Tract Density]
or convert tracks to ROI using [Track][Tract to ROI] and then save the
ROI as nifti file.

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 post to this group, send email to dsi-s...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.

[j.cos...@jatneurolab.com]

Thank you Frank. To update, I am able to save the tracts as Nifti files, though the transformation matrix does not appear to be saved in the nifti file. So, I extracted the transformation matrix from the T1w nifti (that I registered to originally) and applied it using FLIRT -applyxfm.

On Friday, March 23, 2018 at 2:09:37 PM UTC-6, j.cos...@jatneurolab.com wrote:

[yi lei]

Hi, i encounted the same problem. could u please tell me how to extract the transformation matrix?

is there any easy way as I'm not familar with coding

[Frank Yeh]

[Tool][O1 View Images][Header][Set Transformation] -> copy the content and paste it to another to overwrite

[yi lei]

thankyou

and is there anyway to convert nii back to trk?

[Fang-Cheng Yeh]

Sorry there is no way to my best knowledge.
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/eb4566ae-31c9-445c-a2af-2436aaac6b31n%40googlegroups.com.