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Dear Andy,
Downloaded v2.0, getting the same error message as described in this thread. Didn’t solve the issue in april, I figured I’ll wait for the new exiting v2.0, but the same error message persists.
MF
Hi Andy,
Just finished the download from lead-dbs.org or did you mean GitHub?
However, the ea_prefs_default.mat files is located in lead/common. Still the same error message.
MF
Hi,
A quick response a couple of month late, and probably obsolete.
For some IPG and electrode combinations from the Medtronic portfolio, new restrictions applies. Check Medtronic MRI webpage, http://www.mrisurescan.com
For a quick summary, check zrinzio et al 2011 (https://www.researchgate.net/profile/Ludvic_Zrinzo/publication/51569875_Clinical_Safety_of_Brain_Magnetic_Resonance_Imaging_with_Implanted_Deep_Brain_Stimulation_Hardware_Large_Case_Series_and_Review_of_the_Literature/links/02bfe50cc9e3130cae000000.pdf)
The SAR limit is quite hard. 0.4 W/kg is of course better (see Zrinzo link). However, new restrictions makes it possible to use multi-ch head coil, which is preferable for SNR issues. If you have a siemens system, the SPACE sequences could be a good options for 3D resolution T2 images. However, haven’t optimized these protocols at home yet. Think they have a low flip angle and low SAR/B1rms.
MPRAGE is always nice to have post-op. Good 3D image, with no SAR/B1rms issues.
Did a small survey, and B1rms 2 uT, correspond to about mean 0.4-0.5 W/kg, probably good to know.Post-operative restrictions might be changing fast coming years, be sure to check the latest guidelines from the corresponding manufactures website.
/Markus
MRI-PhycisistFirst of all, I experienced some difficulties getting the .m file to work, actually I can seem to get any exported files at all – the folder headmodel is not created either. Though I’m getting the option to do the simulation after pressing the wand button – vat files in nifti format is produced during simulation but these files are just black. Is there any options or procedures that needs to be done before?
And I also have some general questions regarding lead-dbs.
I have been thinking about the scenario using post-op CT, however not as common at my institution but performed anyway from time to time.
Sometimes when manually defining the electrode artifact during reconstruction the images is just black – perhaps its because some pre-processing step is incomplete, I think this phenomena only occur when i skip registration and normalization – just change the postop_ct to lpostop_ct.
Usually I ask our neurosurgeon to manually delineate target structure so the only step i need to take is to register them. But I believe that the black scene appears then as well.Second question. So preferably we do postop MRIs – including a 3D_T1 image and T2w, PD or T2-STIR depending on target. The 3D_T1 is always included and covers the whole brain and cause no problem regarding SAR/B1+rms levels. However, Medtronics updated guidelines give a little bit more space to increase the coverage of the T2w image for example, but not near the T1. But back to the question, do you have any experience segmenting the electrode based on T1w image? I tried it and it seems to work, but having trouble checking cause I don’t get the nifti, of course there should be other ways of confirming but I’m prefer this until I found something better.
And have I understood it correctly that the normalization step is only for getting structures from template to my images. So if I get the manually, this should be necessary? Or would it affect the reconstruction of the electrodes?
And thanks for a really nice software, I’m really curious about it.
Regards
MarkusDear Andy
I read about the script for exporting electrode tips as nifti files. This would be very useful for me – and I like to ask if you please would share.
Kind Regards
Markus Fahlstrom
Uppsala University, Sweden
markus.fahlstrom@radiol.uu.se
