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andreashornKeymaster
Dear Philip,
thanks for letting me know. Yes, the nifti option is another one.
I think 0-3 right/left is a center-wise convention, I fear.
I heard that some centers do it reverse.
I checked whether there is an official guideline but didnt find one. If you have any official document (e.g. Medtronic/Boston specification) stating that 0-3 should be left, I’d be happy to change it (although it would be a rather major hack).Best, Andy
andreashornKeymasterTwo of us will be there, yes. Looking forward to meeting you there, too.
andreashornKeymasterHi Philip,
so at least I wrote a hotfix which should work now.
The easiest option would be to install lead dbs via github as described here:
https://leaddbs.gitbooks.io/leaddbs-manual/content/Installation.html– then it should work. You could delete all ea_stats.mat files within your patient folders just to make sure (although I think this is not necessary).
Alternatively, we’ll probably upload a new minor release soon, too.
Best, Andy
andreashornKeymasterHi Philip,
I think I informed you wrong and stats are not properly built. Will need to investigate a bit more on this.
Best, Andy
andreashornKeymasterHi Philip,
I haven’t used the feature in a while but just tried on a small test dataset and can confirm it worked for me. I guess the problem is that you actually need to add a group connectome to the process even if you are not at all interested in connectivity. I never found the time to support the case of preparing DBS stats only for the VTA.
So please make sure that you have some valid .mat files in your lead/fibers folder. You can e.g. download the 2013 group connectome from our download page here on the site. In theory you can even install it by clicking on the group connectome button from within lead.
Then – since you’re not interested in fibers, choose the thinned out x 500 option as in my screenshot – this wont take a lot of processing time.
Make sure you have entered all stim params for each patient correctly and chosen the Mädler or Kuncel VTA model.
Then click on prep. DBS stats. It will prepare all the stats for all patients. When this is done, you should be able to access the data in the mat files as well. Or you can add a regressor into lead group and e.g. click “Correlation between Regressors and Volume Intersections / Fibercounts” in lead group directly.I think it’s great you’re trying this, it should be done more. One day I may find some time to make lead_group a bit more robust and intuitive.. I guess it’s quite powerful with many features but that also makes it quite hard to use. Also, not all features may always be up to date for the currentmost single-subject processing features. LG used to be a personal tool for quite some time and grew with features I needed at the moment :)
Best, Andy
andreashornKeymasterDear Philip,
yes, lead group is widely undocumented unfortunately, sorry about that.
Before you click “Correlation Between Regressors and Volume Intersections”, you need to calculate the DBS stats, i.e. click on the “Prepare stats” button. I hope this works, haven’t tried for some while – let me know if it doesnt.The info should also be inside the ea_stats.mat file of each patient after that.
Regarding the Accolla atlas, it seems that you have an outdated data folder from an older version than 1.5 – you can simply delete the atlas_index.mat file and it will be regenerated based on the niftis on the next visualization call. Still, I’d suggest to update the datafiles, i.e. make a clean new download from the website.
Re the 2D viz – this seems to be a bug – I guess you could circumvent it by once clicking on the settings dialog of the 2D visualizations and saving these settings. Seems there are no default settings stored in your installation somehow.
Hope this helps, let me know if you have further questions!
andreashornKeymasterHi Philip,
thanks for letting us know. I’ll nevertheless check this bug and try to fix it within the next release.
Best, Andy
06/28/2016 at 11:33 PM in reply to: Processing on post-op ct data with single electrode trajectory #1178andreashornKeymasterMailed you. Will add some more export features in the near future.
andreashornKeymasterHi Greydon,
I fear we are not the best people to ask here. Of course, general imaging principles apply: The better the resolution and signal to noise ratio, the more accurate the results may be.
Maybe you can get some insight here: http://www.ncbi.nlm.nih.gov/pubmed/25113409In any case, I personally prefer T2 sequences over T1 sequences since they show the STN. If possible, 3D sequences with high resolution are optimal. However, more “clinical” acquisitions with high in-plane resolution and larger slice thicknesses are also okay. Up to three post-op sequences can be used in Lead-DBS in combination, e.g. an axial, coronar and saggital acquisition.
Hope this helps,
best, Andy
andreashornKeymasterHi Greydon,
I’d advise to use a full-brain image with the best resolution available. If you have a highres full brain T2, maybe use this one since it shows the STN. Planes don’t really matter, it should be as high-res in all dimensions as possible (I guess an optimal file could e.g. be a 1x1x1mm T2 or T1).
If you use a T1, please name it anat_t1.nii in order that Lead-DBS uses the T1-MNI template for normalizations (this only works with ANTs).dcm2nii is the optimal choice, please export the files in 4D nifti format (.nii ending).
Best, Andy
andreashornKeymasterDear Sahbi,
sorry you are having so much trouble getting it to work.
Usually, the y_ea_normparams.nii file will be generated if you run an SPM-based normalization within Lead-DBS (DARTEL, Segment). However, I’d recommend to use Advanced Normalization Tools for now – it’s just much better tested because we use it ourselves. I’d still like to find out how the problem originated. Could you please do the following:1. Run (only) Normalization again (DARTEL) and check if ea_normparams.nii really isn’t being generated and if so, if an error message appeared. Please always post full error messages (the whole red text in Matlab), otherwise, they are often useless for me.
2. If the file really doesn’t appear, try running the ANTs based normalization and see if things work from here.
If both doesn’t work, we should get in contact via mail and you’d need to somehow send me the dataset in an anonymized way so I could debug and see where the problem originated.
Best, Andy
andreashornKeymasterMh, are you sure you are indeed using SPM12 (and not a different version)? Please make sure that SPM8 is not on your path and if you start spm, version 12 it starts up. This particular check-function (ea_checkfiles) is only working with SPM12 and will show an error if using SPM8 (not supported anymore).
You could temporarily comment line 34 of ea_checkfiles.m and everything should still work.
Best, Andy
andreashornKeymasterOkay. I need to fix this at some point.
In the meantime, please download and unzip this file (https://dl.dropboxusercontent.com/u/18255196/dartelmni_6_hires.nii.zip) and put it into your lead/templates/dartel/ folder. Re-run again. I’d also advise that you run each step separately to be able to debug a bit better if you’re still unfamiliar with the toolbox.Best, Andy
andreashornKeymasterDear Sahbi,
this is weird. Did you try to open SPM 12 itself alone? (i.e. type spm fmri) and see if that starts up?
Best, Andy
andreashornKeymasterHi,
okay.. this is weird. Could you please write me an email? I couldn’t find yours.
Best, Andy -
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