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Great to hear, thanks for the feedback!
Please be aware that there’s limited to no experience in terms of accuracy and methods for the macaque space from our group. If in doubt could be interesting to get in touch with the Neurospin group who helped/drove me to develop a generalization to macaque space.Yes, in the tool, see http://imgur.com/a/6SLuV
I hope it works though, there are not too many people using it. Happy to help if it doesn’t.Hi Jose,
are you referring to the macaque labels? You need to switch space to MNI macaque to download/install that.
Don’t know any other Inia map..Best, Andy
Hi Atefeh,
usually the popup would read “Patient Preop” and “Patient Postop” if available.
I guess since you’re using a dataset with no postop-data, could be that Lead-DBS currently is buggy and doesn’t show the option to visualize the preop data at all.
Bigbrain is a histological dataset by the group of Katrin Amunts.I don’t know any freely available datasets with postop data. I wish these were available, but I fear they aren’t.
Maybe Lead-DBS isn’t the optimal tool for what you are doing?Best, Andy
Hi Atefeh,
it’s true we stripped some options from the anatomy panel but these were not really working before, anyways.
Mainly, these options were meant to export 2D slices into the 3D viewer. We decided to rather make similar functionality available via the 2D export (from the Lead main gui) or in Lead anatomy.You can use the popup menu shown in your screenshots to visualize patient anatomy instead of the MNI template.
Best
Hi Atefeh,
thank you for your message – however it’s a bit hard to find out what (you think) went wrong.
There are so many ways to use Lead-DBS to analyze your data and it is very important that you understand what it actually does to interpret results. For us to help you / explain what’s happening, it’s is similarly important that you let us know what you exactly did.Some basics that might help:
1. Lead-DBS uses atlases to define anatomy. There is no option to subdivide the STN in single patients (although we’re losely working on such things).
2. It is a big difference whether you visualize results in native or template space. In the first option, the atlas is co-registered into native space, in the second case the MRI data of the patient is co-registered into template space (where the atlas is defined).
3. These warps (from native to template and back) are performed using the best nonlinear methods available in the field (e.g. see Klein 2009 NeuroImage) that have been specially tuned to be precise in the subcortex. Still, as in any scientific model, the model has limitations.
4. These limitations are largely driven by the quality of your preoperative imaging data and quality. For instance you can supply 10 different MRI sequences including some special Basal ganglia sequences (FGATIR, QSM etc) of the same patient to Lead-DBS and use *all of them* simultaneously to define the warp e.g. using the Unified Segmentation approach by John Ashburner on a specialized tissue prior model featuring regions of interest (STN, GPi) included in Lead-DBS. If you did that, I’d guess that the nonlinear transform would be really accurate, really showing a precise location of electrodes in relationship to the atlas STN. However, this is an ideal scenario and most Universities don’t have such great preoperative imaging protocols. Rather, in a “standard use case”, most centers have a T1 sequence and a T2 sequence or similar. Often in poor resolution. If you supply this data to Lead-DBS, it will still give you a result but the accuracy is just way worse than in the first case. So part of getting good results are not dependent on the *data* and not the methods of Lead-DBS.
5. A good rule of thumb to find out how precise results could optimally be is for instance whether you can clearly discern the structures of interest on the preoperative acquisition. Say, you cannot clearly see the STN yourself on an image, you’re not totally sure where it starts and where it ends. In such a case, Lead-DBS will not be able to apply some magic and still see the structure, let alone the STN subdivisions. It will make a “best guess” based on surrounding anatomy and the segmentation results but that’s all you can get with poor data.
6. Finally, please be aware that none of the segmentation/normalization techniques have been developed by ourselves. We use freely available tools and sometimes tweak them a bit for subcortical anatomy. All these methods are published and well documented. It is highly recommended to study how these methods work, what their benefits are and their limitations.Now getting maybe a bit closer to your problem: You described “all images looked the same”. If you mean the visualization of anatomy in the 3D viewer, it could have been that the MNI template was displayed instead of patient specific anatomy? This is the default setting. You can visualize patient anatomy by choosing what to display in the anatomy slices panel. Maybe this helps?
Best, Andy
See here:
I don’t have any ready-made .zip files from before but you can get the code from any release there on github.
However, I’m pretty sure that this is not the reason. We and other labs use Lead-DBS a lot on a daily basis and we don’t get this error. I would have definitely heard of this error if it had to do with the current release.Rather than going back I’d even recommend going forward by installing via github (see ) and you’d get the newest features and we can much easier fix small issues that may occur.
Also, would really recommend to do a complete clean install, i.e. deleting all Lead-DBS related code (including the .ea_prefs.m file in your windows user home) and then installing freshly either from website or via Github.
Best, Andy
I think now you deleted the ea_prefs.m inside the Lead-DBS folder. I meant a hidden file called .ea_prefs.m (starting with a dot) in your Windows home directory.
Weird. Can you delete (or move somewhere) the file in your home folder called .ea_prefs.m?
Then restart lead and try again?No I meant to add a breakpoint. For instance you can write the word “keyboard” on that line, save the file and try normalization again. Then Matlab will stop at that particular line, showing you a K> symbol in the command prompt.
Then enter “anatpresent” there and let me know what it says.Btw just tried to reproduce the error here but works fine on my side.
Best, Andy
Okay, thanks! Can you please set a breakpoint after line 56 in ea_normalize_ants and tell me how the variable “anatpresent” is defined? It should be a cellstring with a single entry {‘anat_t2.nii’}.
Can’t really help you without that information though.. Need some more info to reproduce this and debug.
Does this only happen for this specific patient or for all patients you tried?
Okay. Then it seems that the files in your subject directory are not named correctly. Can you tell me which files you put into the patient’s folder?
Also, has it worked for you in the past?
Best, Andy
