[andreashorn]

Hi Ada,

sorry for the problems,

the “acpc” bug is already known and will be fixed in the next release. In the meantime, please comment (add a ‘%’ in front) line 39 in the ea_load_reconstruction.m file to make it work.

Re. your first error, these are no errors and you should be fine. However, in case nothing happens, please make sure you find a file called “mni_wires.mat” inside lead/templates folder.
If you don’t, you can download the file here (https://dl.dropboxusercontent.com/u/18255196/mni_wires.mat) – or redownload lead-dbs from the website.

Best, Andy

[andreashorn]

Hi Tobias,

thanks so much for your nice feedback!

However, for your question, a software like DSI Studio or Trackvis would be much more ideally suited. It’s quite straightforward to do what you want to do in these two tools at least (very likely MRTrix or ExploreDTI can do this, too).

Best, Andy

[andreashorn]

Oh okay – sorry for not getting that.

could you again send me the error that shows up? Unfortunately, in your message from 6:59 the crucial first line is missing :(

sorry that this is so complicated. It really should work well, usually..

Best, Andy

[andreashorn]

Weird. Could you send me the general error (when uncommenting the lines)

The snippet in your last message is just a warning (no error).

Best, Andy

[andreashorn]

Hi Katherine,

did you re-uncomment the lines we commented before?
Probably that’s the reason.

Best, Andy

[andreashorn]

Okay, thanks! Seems you are using a different zscore script which is masking the original Matlab one.
If you type
which zscore
you will see which file Matlab uses when zscore is called. You could then rename/delete that file if it’s not relevant for other projects and/or remove it from the Matlab path.

Then it should work I guess – and you could afterwards uncomment the lines again.

Best, Andy

[andreashorn]

Sorry Katherine,

the line numbers I told you were wrong.. Please revert the changes made and instead comment out lines
22 as well as 114-116 – and send me the error that will pop up then.

Best, Andy

[andreashorn]

Dear Katherine,

sorry to hear – two things:
1. please completely ignore the warning about the Image Calculator. It’s actually a “feature not a bug” we abuse the SPM Image Calculator to get images into the exact same space. It’s misleading for users, of course, and I wanted to disable the warnings for a long time already.. But in general you can safely ignore all warnings in Lead-DBS..

2. Regarding the error – it seems to happen in the “Show Normalization” Step (not in the actual normalization process). So I think images should have been normalized. You could check e.g. with SPM check coreg or 3D Slicer whether gl*.nii files are in MNI space (e.g. compare them to the file mni_hires.nii in the lead/templates/ folder).

It’s still very weird that you cannot visualize normalization directly in Lead-DBS.
To debug, could you please comment lines 22 and 126-128 in ea_show_normalization and rerun the “Check Normalization” Step only?
Post the error message here then if you get the chance.

Best, Andy

[andreashorn]

Hi there,

you can re-run “Normalize” with a different setting (e.g. “Coreg MRIs: Hybrid SPM & ANTs) in the coreg popup and choosing “(Re-)apply (priorly) estimated normalization.” in the Normalization popup.

Since coregistrations are affine (nonlinear), it’s okay to mix methods in this step IMHO.
If none of the options coregister your images nicely, you could try to manually coregister the postops to preops e.g. using 3DSlicer.

Best, Andy

[andreashorn]

Hi Ramin,

I fear trying to show the whole connectome in Lead-DBS is not so easy – Matlab is not really built for this and in any case Lead-DBS isn’t at the moment.. However, just to have a good look at the whole fibers I recommend to use trackvis (www.trackvis.org). There is a file called FTR.trk inside your patient’s folder which you can load in trackvis to show fibers.
Within Lead-DBS, the way to go would be to visualize only the fibers traversing through a volume of activated tissue.
This video walkthrough goes through the whole process:

Just instead of selecting a group connectome in the convis viewer in the end, select “Patient specific fiber tracts”.

I hope this all works..
Finally, you can also do stats on fibertracts connecting your VTA with other areas in the brain. I.e. find out whether differences in connectivity code for clinical outcome or similar. You can do some of that stuff directly using lead group – which is, to be honest, very unintuitive.. Sorry about that.. trying to improve everything but lack the time and manpower for now..

Best, Andy

[andreashorn]

Hi Ramin,

honestly, it’s quite possible that the deterministic tracker has issues with some datasets, it’s not well tested and I wouldn’t advise to use it at all (will remove it from Lead-DBS at some point). It’s real diffusion tensor imaging (i.e. with the tensor model) and that’s quite outdated.
The Gibbstracker sometimes takes >1 day but should not take 5 days (except it’s a really huge dataset or something similar). Does it still produce fibers at all? There should be a window that opens which should show you progress. If that’s not the case (i.e. no new window popped up), please abort Matlab and paste the error code here (i.e. where Matlab was hung when you aborted).
Also, there should be a third option which is to use DSI studio under the hood (it’s referred to as generalized Q-imaging (by Fang-Cheng Yeh)). It’s an extremely fast and also modern fiber tracking method which should work on all datasets (i.e. single- or multishell). Can definitely recommend that method – but also can recommend the Gibbstracker (which takes ~4-8 hrs. for one subject on a modern computer).

Also, please use the currentmost version of Lead-DBS since we fixed some fibertracking related things in the recent past.

Let me know if that helps!

Best, Andy

[andreashorn]

Great, thanks for letting us know!

[andreashorn]

Hi Rafael,

sorry to hear. I just finished uploading a new release which should fix this issue.
Let me know if it still happens!

Best, Andy

[andreashorn]

Dear Phil,

unfortunately, I guess, there’s no better solution at present. In case you have any ambition to fix this, please do – it shouldn’t be too complicated. Just lack the time myself for now.
Lead Group should be considered a long-term beta, unfortunately..

Best, Andy

[andreashorn]

Hi Markus,

Regarding export from electrodes to nifti: Would it help you to be able to export to a different surface format?
E.g. you can import .ply files in nearly any 3D visualization software including 3D Slicer and SurfIce. To export to .ply format, select the patients in Lead-DBS and then choose Export -> PLY from the Tools Menu of the main Lead GUI.

Exporting to nifti in general is not the best idea since electrodes are not the best option to be voxelized (they are small and you’d need high resolution to do so). However, you could convert the .PLY files to a voxelized version e.g. using Iso2Mesh by Qianqian Fang: http://iso2mesh.sourceforge.net/cgi-bin/index.cgi

Re the CT question: It’s not supported to rename files to l* or gl* anymore since Lead-DBS now reconstructs electrodes hybridly in native and MNI space. This may have worked in some early versions but doesn’t work anymore. Also, please note that any l* or gl* file needs to be in MNI space (!). That’s basically what l* and gl* prefixes stand for.
You have two options: 1. place a postop_ct.nii alongside your anat.nii or anat_t1.nii file into the folder and do co-registration between postop_ct and the primar anat file in Lead-DBS. This will generate the rpostop_ct.nii which will then be warped into MNI space in the normalization step.
2. place an rpostop_ct.nii alongside your anat.nii or anat_t1.nii into the patient folder. Lead-DBS will assume that the two files are exactly co-registered, i.e. have the same voxel resolution and nifti-header matrix.
After this, you need to run a valid normalization step. I’d recommend to use the ANTs SyN approach or if you have multiple anatomical files (e.g. anat.nii (=T2), anat_t1.nii (=T1), anat_pd.nii (=PD) and dti.nii (will generate fa2anat.nii file and white-matter anisotropy will be used for normalization, too) the ANTs Multimodal approach.
You can of course program your own normalization routine if you want things to be warped differently. It may not be completely trivial but if you’re good at programming, it’s doable. Any file called ea_normalize_*.m will be recognized by the Lead-DBS GUI.

Re the second question: I’d always prefer T2 for postop but T1 works as well. You can also call your postop t2 “postop_tra.nii” and your t1 “postop_cor.nii” and both will be normalized into MNI space. You can then swap image names to see which gives you the better precision in the manual reconstruction step.

Finally, as described above, the normalization step is an integral part of the Lead-DBS routine, so you definitely need to perform it. Nothing will work if you don’t. Still, this doesnt limit you to working inside MNI space. You can visualize results in either MNI or native space lateron. Since Lead-DBS has originally been designed as a research tool, MNI space based routines are much better maintained and tested.

So to answer your question, no, normalization is not only used to get structures to your image.

Hope this helps! Let me know if you have further questions!

Best, Andy

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