[andreashorn]

Sure, no problem!

[andreashorn]

Please replace this file: https://dl.dropboxusercontent.com/u/18255196/ea_firstrun.m

[andreashorn]

Hi Ada,

the lines you wrote are just a warning and totally fine. There’s no real “error” in there.
Maybe you just need to wait a bit longer?
When visualizing an atlas for the first time, Lead-DBS needs to build several structures and files first.

Best, Andy

[andreashorn]

Hi Ada,

the lines you wrote are just a warning and totally fine. There’s no real “error” in there.
Maybe you just need to wait a bit longer?
When visualizing an atlas for the first time, Lead-DBS needs to build several structures and files first.

Best, Andy

[andreashorn]

Hi neuropsyched,

sorry, I think this really was a visualization bug – it showed the MNI space backdrop but the atlas in native space. Atlas file should be fine, visualization of the backdrop not.

Please exchange this file:
https://dl.dropboxusercontent.com/u/18255196/ea_assignbackdrop.m

Best, Andy

[andreashorn]

Sure, if you are visualizing in native space, it’s all in native space, i.e. the original anat_t1.nii will be visualized, as well.

[andreashorn]

This is really weird.

What you could do is delete /patient/atlas/native folder and retry to visualize just to make sure this will be generated again as flawed as before.
If this doesn’t help, if possible, could share the subject with me so I can try to replicate here?

Best, Andy

[andreashorn]

Hi Ettore! At least if you just updated to the newest version I fear this is a Matlab version issue. Or do you use ML >2014a?

In any case, you can always check coregistration somewhere else (I like 3D Slicer for it).
The files to check would be rpostop_ct.nii and anat_t1.nii or anat_t2.nii (the one you used or either one if used both)

If check normalization also fails, you should compare the glanat* files to the /templates/mni_hires*.nii series (which are the 2009b NLIN asym templates).

Hope this helps and best regards to Fribourg!

[andreashorn]

The HO atlas is already supplied as a “labeling” scheme in Lead-DBS so you could also use the single line:
>> ea_labeling2atlas(‘Harvard Oxford Thr25 2mm Whole Brain (Makris 2006)’)
to convert it into a subcortical atlas. This only works perfectly sometimes but it surely extracts all the labels as single files for you. When I just tried it here, I e.g. had to copy the file Left_Occipital_Pole.nii from the /midline subfolder to the /lh subfolder of the converted atlas set.

Alternatively, you can look at how other atlases are stored in Lead-DBS to find out how they should look like. Basically, each structure needs to be a single file and can be inside the /lh, /rh, /midline or /mixed subfolder. If e.g. the same homologue structure for lh and rh is stored in a single file, put it in mixed and lead-dbs will divide data at x=0mm.

Finally, it’s important to note that Lead-DBS uses the MNI 2009b NLIN 0.5×0.5×0.5mm space whereas FSL essentially doesn’t (it uses the older 6th gen nonlinear space).
Differences are small but can be significant in DBS imaging (read more about this issue here: http://www.lead-dbs.org/?p=1241).

Hope this helps,

best, Andy

[andreashorn]

Hi there,

two questions:
1. Did you check co-registration and normalization and did both look correct?
2. Did you by chance use FNIRT (FSL)? Because it could be that the inverse FSL routine is currently not working correctly.
-> If not, which normalization method did you use?
How many preoperative files did you use (i.e. was it only the T1 or is there additional data in your project)?

Best, Andy

[andreashorn]

Hi Philip,

the DISTAL atlas empty folder was released as a mistake. Unfortunately, the atlas paper is still under review (preprint here). Soon after that, we’ll make it available.

Best, Andy

[andreashorn]

Hi Philip,

sorry to hear – adding to Ningfei’s comment, as announced in the newsletter, we changed the naming scheme of anat.nii to anat_t2.nii by default. Lead-DBS should however take care of this for compatibility reasons (i.e. rename anat.nii to anat_t2.nii) and it is weird that it didn’t work in your case.

It’d be awesome if you could follow Ningfei’s directions and paste the output here.

Best, Andy

[andreashorn]

Hi Markus,

the algorithm stops at -15.5 mm but that is just a line of the electrode trajectory, it doesnt say anything about the electrode position itself. You can use the coordinate of the lowermost contact (e.g. for right hemisphere stored as reco.mni.coords_mm{1}(4,:) in ea_reconstruction.mat – {2} is left hemisphere). Based on the next contact (coords_mm(3,:)) you could then easily compute the position of the tip (if you have the electrode dimensions).

For zona incerta I only know the Chakravarty atlas but it features the whole thing (not caudal ZI – handled as target for PD by e.g. Blomstedt/Plaha (but see Schmitz-Hübsch 2015 MDS and Welter 2014 Neurology) or the “zona incerta” some people refer to as the subthalamic area – handled as target for ET).

Hope that helps!

Best, Andy

[andreashorn]

Hi Ada,

glad it worked.
What you could do is i) try with a “manual” entrypoint, i.e. set the popup menu to “manual” before running the pre-localization step. You’ll be prompted with a window in which you may click on the electrodes within a red rectangle.
If you don’t see the electrodes at all, something went wrong in normalization.
ii) try with another patient – just to verify it works in general on your side. If that works, we can definitely fix it for the current patient, as well.

Best, Andy

[andreashorn]

Dear Weidao,

sorry for the late response, am traveling.
It seems that your Matlab has no write permissions within the lead-dbs installation folder, i.e. lead dbs seems to be installed on a “read only” disk or similar. Could you move it to somewhere where your Matlab installation has write access or fix permissions and try again?

Best, Andy

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