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My email ID is ajoshi@sipi.usc.edu. You are using 64 bit windows platform, right?
Can you try running the surface extraction sequence again? My guess is that for some reason .warp file is corrupted leading to the error in later stages. If it is possible for you to share the data with me, I can try running it.
Hi Xu, Is your data on external hard drive? If yes then can you please try copying it on internal drive and then running the program? The speed of the external drive may not be enough for data processing. Please let me know.
The SVReg registration module performs full anatomical alignment of subject to atlas. This alignment is much more accurate than AC-PC alignment. Can you please explain some more about why you want to do AC-PC alignment? Is it for visualization purpose?
Hi Luca, Are you using Linux/Mac/Windows? There is a bias filed correction script now included with BrainSuite 16a. It is in C:\Program Files\BrainSuite16a\svreg\bin\gui_bias_correct.exe .
Are you using this?Currently, to my understanding, closing BrainSuite or opening a new instance is the cleanest and probably the only way to start processing a new volume.
Can you make sure that there is sufficient memory available (~4GB)? You can resume the processing steps by Load original MRI in BrainSuite, then Cortex->Cortical Surface Extraction. Then click Cortex->Pial surface extraction. Click restore from previous and select the original mri. Now you can click in the min dialogue box of Cortical Surface Extraction to continue the process.
This generally happens if there is some abnormality in the data or one of the previous processing steps before the topology correction steps have failed. Please check if the outputs upto that point are reasonable. If possible it would be good if you share a screenshot just before topology correction when it fails.
Hi Francois,
Yes, the default parameters work better for this volume and I deleted the comment about parameter change.
Thanks,
AnandAccording to the following link, it should not matter, but it also says the following.
Windows
To run deployed MATLAB code against MATLAB Runtime install, mcr_root\ver\runtime\win32|win64 must appear on your system path before matlabroot\runtime\win32|win64.
If mcr_root\ver\runtime\arch appears first on the compiled application path, the application uses the files in the MATLAB Runtime install area.
If matlabroot\runtime\arch appears first on the compiled application path, the application uses the files in the MATLAB installation area.It is worth trying to set environment PATH variable such that MCR appears before Matlab.
Hi Francois,
Thanks, if you are using windows system, then the compiled exe will figure out the path for MCR or Matlab runtime automatically, based on registry keys I think, but for Linux and Mac, one has to do some modifications to the svreg script.
I have never seen this error before and cann’t reproduce it here, so not sure how to proceed. I am trying it on another computer. If you have any suggestion on how to reproduce it here it would be helpful. Since the error came from settings of image processing toolbox, did you have any change in setting for that toolbox?
AnandHi Francois,
I am running SVReg sequence on the data that you shared and it is running fine. Do you have full Matlab or MCR for 2015b installed at the default location? Perhaps, one thing to try is that you have Matlab MCR for 2015b installed in default location. If you have any suggestions on how I can reproduce this error, that would be helpful. Do you have anything special in your Matlab/Windows installation (added third party library etc)? AnandHi Francois,
I tried the volume you shared and it ran fine with all default parameters (no change in skull extraction or other parameters).
Can you try with default parameters and if it fails, can you please share the directory with all the outputs generated up to that point? I will try to see if I can figure out where things are diverging compared to my run on the same subject.
Thanks,
Best,
Anand
