[bjvillegas]

I am running El Capitan with all updates installed (brainsuite15c, quartz2.7.8, MCP2012A) but get error relating to “Time Machine” when the automated SVREG gets to splitting the hemispheres. I am also trying to run Brainsuite on parallels in my Windows partition and there I get an error in which the (SVREG.hemi.XXXX.exe) app crashes. SVREG seems as if it is installed correctly but still seems to crash. I am also running on Windows 7 and installed all the appropriate components. I am trying to segment an MRI scan b/c I am also working on the pathology of the brain and am trying to correlate my in vivo PET signal to my in vitro IHC. Any help would be appreciated. I have tried all the recommendations on the Brainsuite site but have been unsuccessful. Both seem to be failing at the hemisphere labelling step. On my MACOSX Brainsuite I am getting the following error message:

“2016-04-23 10:40:36.470 svreg_label_surf_hemi[3119:93338] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2016-04-23 10:40:36.472 svreg_label_surf_hemi[3119:93338] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2016-04-23 10:40:36.472 svreg_label_surf_hemi[3119:93338] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2016-04-23 10:40:36.473 svreg_label_surf_hemi[3119:93338] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2016-04-23 10:40:36.473 svreg_label_surf_hemi[3119:93338] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2016-04-23 10:40:36.474 svreg_label_surf_hemi[3119:93338] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2016-04-23 10:40:36.475 svreg_label_surf_hemi[3119:93338] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2016-04-23 10:40:36.475 svreg_label_surf_hemi[3119:93338] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
2016-04-23 10:40:36.476 svreg_label_surf_hemi[3119:93338] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported.
Labeling left hemisphere
Computing mid cortical surfaces
Checking Euler Characteristic of input surfaces, it should be 1
{Attempted to access s.faces(:,1); index out of bounds because
size(s.faces)=[0,0].
Error in euler_number_mesh (line 26)
Error in svreg_label_surf_hemi (line 131)
}
MATLAB:badsubscript”

[David Shattuck]

There are two issues here — the one with Time Machine and the processing error in SVReg. They are unrelated.

For the time machine issue, this is an issue with Matlab. If you run a Matlab program once from the command line using sudo, this will fix this (see this old post on Mathworks, for example: http://www.mathworks.com/matlabcentral/answers/18762-annoying-matlab-start-up-warnings-on-mac-matlab_maci64-attempting-to-exclude-an-item-from). E.g.,

sudo /Applications/BrainSuite15c/svreg/bin/svreg.sh your_subject_file

The other issue has something to do with the surface model. Did the models look okay in the GUI?

It may be easier to address the specifics of this issue via email — do you want to email us at support@brainsuite.org?

thanks,
David Shattuck

[Anand Joshi]

I agree with David that the first issue related to time machine warning should be fixed by running Matlab using sudo as he explained. As such this should not affect the rest of the processing and you can safely ignore that warning.
Regarding the second issue related to the error during svreg processing, I think the surfaces are not probably extracted correctly. Before running SVReg, did the surfaces look like the ones shown in the screenshot below (right bottom windows)?
http://brainsuite.org/wp-content/uploads/2015/01/hemisplitpic.png

If you can post or email me a screenshot that will help in addressing this.

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