Dear Lead-DBS team,
I’m using Lead-DBS / Lead Connectome v3.2 on Windows and I would like to warp my own existing tractography file (.trk) from subject (native) space into the Lead-DBS template space (MNI152NLin2009bAsym / ICBM 2009b NLIN Asym).
Context:
I already ran “Normalize Volumes” with ANTs in Lead-DBS for this patient, and Lead-DBS shows “Normalization has been done.”
My goal is only to transform an existing tractogram (.trk) into MNI2009b space for visualization/atlas alignment. I do not want to re-run fiber tracking or recompute SC in Lead Connectome.
Issue:
Older forum answers mention using Tools → “Apply to File” with the ANTs deformation (.h5) to warp fibers to MNI, but in v3.2 I don’t see an “Apply to File” entry.
In the v3.2 Tools menu I see options like:
“Map file from anchor space to template…”
“Map file from untouched anchor space to template…”
and the reverse directions.
However, I’m unsure whether these options support .trk files (or only NIfTI volumes), and which one is the correct choice for tractograms.
Questions:
In Lead-DBS v3.2, what is the recommended GUI workflow to warp an existing .trk tractogram into MNI152NLin2009bAsym?
Do the Tools menu items “Map file from anchor space to template…” / “Map file from untouched anchor space to template…” support .trk? If not, what is the official way to import/wrap patient-specific fibers?
If the correct method is to apply the ANTs deformation field from the patient’s normalization, which specific file(s) should be used (e.g., which .h5 / warp in derivatives/leaddbs//normalization), and in which direction (native→template)?
Are there any requirements about the tractogram’s space/orientation (e.g., must the .trk be in the Lead-DBS “anchor space” corresponding to anat_t1, or can it be in diffusion space)?
If you have a short step-by-step instruction (or a pointer to the correct documentation section) for v3.2, that would be extremely helpful.
Thank you very much for your time and for maintaining Lead-DBS.
Dear Lead-DBS team,
I’m using Lead-DBS / Lead Connectome v3.2 on Windows and I would like to warp my own existing tractography file (.trk) from subject (native) space into the Lead-DBS template space (MNI152NLin2009bAsym / ICBM 2009b NLIN Asym).
Context:
I already ran “Normalize Volumes” with ANTs in Lead-DBS for this patient, and Lead-DBS shows “Normalization has been done.”
My goal is only to transform an existing tractogram (.trk) into MNI2009b space for visualization/atlas alignment. I do not want to re-run fiber tracking or recompute SC in Lead Connectome.
Issue:
Older forum answers mention using Tools → “Apply to File” with the ANTs deformation (.h5) to warp fibers to MNI, but in v3.2 I don’t see an “Apply to File” entry.
In the v3.2 Tools menu I see options like:
“Map file from anchor space to template…”
“Map file from untouched anchor space to template…”
and the reverse directions.
However, I’m unsure whether these options support .trk files (or only NIfTI volumes), and which one is the correct choice for tractograms.
Questions:
In Lead-DBS v3.2, what is the recommended GUI workflow to warp an existing .trk tractogram into MNI152NLin2009bAsym?
Do the Tools menu items “Map file from anchor space to template…” / “Map file from untouched anchor space to template…” support .trk? If not, what is the official way to import/wrap patient-specific fibers?
If the correct method is to apply the ANTs deformation field from the patient’s normalization, which specific file(s) should be used (e.g., which .h5 / warp in derivatives/leaddbs//normalization), and in which direction (native→template)?
Are there any requirements about the tractogram’s space/orientation (e.g., must the .trk be in the Lead-DBS “anchor space” corresponding to anat_t1, or can it be in diffusion space)?
If you have a short step-by-step instruction (or a pointer to the correct documentation section) for v3.2, that would be extremely helpful.
Thank you very much for your time and for maintaining Lead-DBS.