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Hi astrid,
could you try to replace “radtodeg” with “rad2deg” in line 61 in ea_mapelmodel2reco?
Best, Andy
Hi Xiaoyu,
as Ningfei said, sorry for the outdated manual.
We used to have a proper “macaque toolbox” in the past but now generalized the workflow in lead-dbs to be (in theory) able to work in any stereotactic space you want. One could even easily add a mouse or rat space (although I think noone did that, so far). The macaque space we provide (via web-download from within the space menu in Lead-DBS) is the macaque MNI space. [You could more or less easily add a custom macaque space if you prefer so.]
So as Ningfei said, you can download the macaque MNI space from the space menu. Now we both don’t do any macaque research and probably can’t help much with macaque-specific questions. Officially, the group of Béchir Jarraya at Neurospin in Paris use and support the macaque part of Lead-DBS (you could mail to Jordy Tasserie for questions).Hope this helps and hope it works!
Hi Markus,
that’s weird. So basically this happens if Lead-DBS (=Matlab) doesn’t have write access to either the directory in which Lead-DBS is installed or the user home. On OSX, usually, the home directory should be fine. So could be you installed lead-dbs on a drive with read-only permissions?
Another thing is that everything should still work fine but would use default preferences, i.e. ignore the user preferences. Did you modify prefs at all? You can do so by using the [Tools] menu (-> will migrate to [Preferences] menu soon) [Edit Preferences file…].
If you don’t need to edit any prefs and are happy with defaults you could just ignore the warning.Hope this helps!
Best, Andy
Hi Markus,
sorry, I think the error message is misleading. Could you check whether there is a file called ea_prefs_default.mat inside lead/common/ folder? If not, move the file from the lead base directory to the common subfolder.
That should fix it.
Alternatively, Ningfei made another small release yesterday that should fix it – so you could just press the download button.Best, Andy
Hi Tushara,
again thanks for the hack. The file ea_prefs_default.m should be in the common folder, as well.
I just pushed to Github, I think this will become a hotfix soon.Best, Andy
Hi Thushara,
thanks for the hack. I think we already fixed this on Github.
Lead-DBS copies the ea_prefs_default.m file to users Home directory so one can edit personal preferences. If the home directory doesn’t exist or it doesn’t find it as in your case, I guess it is hard for us to fix. However, for now, Lead-DBS would then always use default preferences (instead of calling the user file).Best, Andy
Yes, they need to be called .bval and .bvec. Alternatively, you can change these naming conventions to suit your needs in the preferences file ([Tools]->[Edit Prefs file]).
Best, Andy
Hi Vinit,
we should in fact remove the deterministic fiber tracking module from Lead-DBS because it is a very basic, even tensor based method (https://www.mathworks.com/matlabcentral/fileexchange/21130-dti-and-fiber-tracking) that hasn’t been used in a while. It is well possible that the method is broken.
Please try to run the GQI method instead which uses Fang-Cheng Yeh’s / DSI studio’s generalized q-sampling imaging and supports multishell data (such as from HCP). It is also deterministic and performed best in a recent open competition (http://biorxiv.org/content/early/2016/11/07/084137).For multishell data, this is clearly the method of choice of the ones implemented in Lead-DBS.
Best, Andy
Hi Greydon,
sorry for that, please run [Install] [Apply Hotfix] – this has already been fixed.
Best, Andy
Hi Vinit,
I am at IBAGS in Mexico and don’t seem to have a good connection with our server. I did upload the group connectome to Dropbox and Ningfei will put it on the Server from Germany – will let you know once it’s uploaded.
Thanks for your patience!
best, Andy
Hi Vinit,
then the deformation is a .h5 file as created by ANTs. You could simply use this entry from the Tools Menu to warp your fibers into MNI:
Best, Andy
Hi Vinit,
the deformation into MNI is nonlinear, so a 4×4 matrix would not suffice. There are deformation files in the patient folder with naming schemes depending on which method you used in the normalization step. You can apply the deformation to other nifti files using the Tools menu.
Best, Andy
Hi Vinny,
the Mädler & Kuncel models only support monopolar stimulations.
We are working on a FEM-based model in Lead-DBS that would support any kind of stimulation but that is not publicly available yet. If you do urgently need such a model for your research you can contact me to think about a collaboration on this – the reason being that the new model still needs a lot of support, is buggy, etc.I’d estimate we will release the model publicly in ~5-6 months.
Hope this helps.Best, Andy
