[ningfei]

Hi, this issue has been resolved and will be included in the new release. But I suggest you to update macOS to at least 10.13 version. It won’t affect ANTs, but for some other tools shipped with LeadDBS (for example DSI Studio), the minimum OS requirement might be 10.13+.

[ningfei]

Hi, this is probably a OS version compatibility issue, since ANTs was built on a newer macOS system. Will try to fix it for the next release which will come soon.

[ningfei]

Hi Tomas,

This is an known issue which has been fixed in the development version. You can download the hotfix from http://www.lead-dbs.org/release/download.php?id=hotfix which is updated several times everyday. Just extract the hotfix and overwrite into your leaddbs installation folder. You can also do it from the leaddbs “Install” menu via “install development version of leaddbs”. Let me know if you still have problem with VTA calculation. Btw, if you see error about intersection when you calculate VTA, you can try to uncheck the “use atlas” optin in teh vta setting window.

Cheers,
Ningfei

[ningfei]

Hi Rubens,

As I checked, that connectivity metrics popup in lead group unfortunately only supports dMRI connectomes for now… The one you chose was a fMRI connectome.

Best,
Ningfei

[ningfei]

Hi Tomas,

From the contents in your MNI_ICBM_2009b_NLIN_ASYM/dartel folder as you showed, it seems the function ea_create_tpm_darteltemplate (which will generate all the dartel and shoot files) didn’t run through. Maybe you can delete the folder MNI_ICBM_2009b_NLIN_ASYM/dartel and the file MNI_ICBM_2009b_NLIN_ASYM/TPM.nii, and run ea_create_tpm_darteltemplate again from MATLAB command window. You can then send me the full log. I will check out what’s happening during the template generation.

Best,
Ningfei

[ningfei]

Hi Maria,

I guess there’s no detailed manual for now on how to create your own electrode model…It’s usually not that difficult, but one needs to be very exprienced in matlab and leaddbs to do that. Those SDE ones were what I created for our collaborator. So your electrodes are similar to SDE-08 S8?

Best,
Ningfei

[ningfei]

Hi Maria,

I see…This actually could be the reason why it’s not easy to detect them. Then maybe only Manual method could help. For the SEEG, you probably also need to use the Manual method or the Slicer Manual method. Correct eletrode model matters, but not so important for the reconstruction. Which model do you have?

Best,
Ningfei

[ningfei]

Hi Maria,

I meant you can use the TRAC/CORE or Refined TRAC/CORE method, but set the Target to Manual, click the electrodes location, then LeadDBS will do the rest. Did this work for you?

Best,
Ningfei

[ningfei]

Hi Maria,

The warnings could be safely ignored I guess. For the mask out of bounds error, you may try to set the Target to Manual and see if it works. Besides, which method did you use for reconstruction? Is it PaCER? Usually it simply works.

Best,
Ningfei

[ningfei]

Hi Heather,

You can’t allocate the memory manually. The program will do it during running. The error you got indicates that you haven’t enough memory in your computer. You need at least 16G RAM (or even larger) to run ANTs based normalization.

Best,
Ningfei

[ningfei]

Hi Monique,

You need to manually set options properly for custom script. Which field of options doesn’t exist when you tried?

Best,
Ningfei

[ningfei]

Dear Monique,

Please check the function ea_reconstruction2acpc (in which ea_native2acpc is called). You just need to set proper options.root, options.patientname and options.sides to make it work.

Best,
Ningfei

[ningfei]

Hi,

Please check the toolbar of 3D scene window. There’s a MER button there. When the control window pops up, the 3D scene will be updated,

Best,
Ningfei

[ningfei]

Hi Hao,

No, ‘glpostop_ct.nii’ is calculated based on ‘rpostop_ct.nii’. It’s a two-step normalization: ‘postop_ct.nii’ -> ‘rpostop_ct.nii’ (aligned with anat_t1.nii) -> ‘glpostop_ct.nii’ (nomalized to MNI space). Since it’s the normalization of ‘postop_ct.nii’ in the end, I think it make sense to use ‘glpostop_ct.nii’. See in your preference file (Lead-dbs menu -> Preferences -> Edit Preferences File). ‘prefs.ctnii_coregistered’ and ‘prefs.gctnii’ are defined there.

Best,
Ningfei

[ningfei]

Hi Hao,

As you may already know from the images, ‘gl’ files are normalized image, ‘tp’ means ‘tone mapped’ image and ‘rpostop_ct.nii’ is coregistered image.

Best,
Ningfei

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