Epileptogenicity map problems

Bugs
1

HI, I wonder if anyone can give me an insight into this problem:
Trying to analyse a recently recorded patient co-registering the MRI and the post-implantation CT. When co-registering/reslicing the 2 dataset for the standard pipeline everything seems to work ok. If I use the same images (.nii.gz for both) within the epileptogenicity map I get a series of errors and the program gets stuck at "generating canonical surfaces" after performing the following ok

iteration 1...
0.9494 0 0 0 0 0 | -1.0565
0.9494 -2.199 0 0 0 0 | -1.0569
0.9494 -2.199 -15.3 0 0 0 | -1.0729
0.9494 -2.199 -15.3 -0.08123 0 0 | -1.0772
0.9494 -2.199 -15.3 -0.08123 -0.02434 0 | -1.0777
0.9494 -2.199 -15.3 -0.08123 -0.02434 0.0009451 | -1.0777
iteration 2...
1.063 -2.199 -15.3 -0.08123 -0.02434 0.0009451 | -1.0777
1.063 -0.8574 -15.3 -0.08123 -0.02434 0.0009451 | -1.0795
1.063 -0.8574 -14.83 -0.08123 -0.02434 0.0009451 | -1.0797
1.063 -0.8574 -14.83 -0.05506 -0.02434 0.0009451 | -1.0804
1.063 -0.8574 -14.83 -0.05506 -0.02326 0.0009451 | -1.0804
1.063 -0.8574 -14.83 -0.05506 -0.02326 0.0009451 | -1.0804
1.144 0.09979 -14.5 -0.03638 -0.02249 0.0009451 | -1.081
iteration 3...
1.32 0.09979 -14.5 -0.03638 -0.02249 0.0009451 | -1.0811
1.321 0.1149 -14.5 -0.03609 -0.02248 0.0009451 | -1.0811
1.321 0.1149 -15.17 -0.03609 -0.02248 0.0009451 | -1.0815
1.321 0.1149 -15.17 -0.02168 -0.02248 0.0009451 | -1.0817
1.321 0.1149 -15.17 -0.02168 -0.01316 0.0009451 | -1.0818
1.321 0.1149 -15.17 -0.02168 -0.01316 0.006235 | -1.0818
iteration 4...
1.533 0.1149 -15.17 -0.02168 -0.01316 0.006235 | -1.0819
1.576 0.6281 -14.99 -0.01167 -0.01275 0.006235 | -1.0823
1.576 0.6281 -15.16 -0.01167 -0.01275 0.006235 | -1.0823
1.576 0.6281 -15.16 -0.01167 -0.01275 0.006235 | -1.0823
1.576 0.6281 -15.16 -0.01167 -0.009584 0.006235 | -1.0824
1.576 0.6281 -15.16 -0.01167 -0.009584 0.006235 | -1.0824
iteration 5...
1.68 0.6281 -15.16 -0.01167 -0.009584 0.006235 | -1.0824
1.685 0.6843 -15.14 -0.01057 -0.009539 0.006235 | -1.0824
1.685 0.6843 -15.22 -0.01057 -0.009539 0.006235 | -1.0824
1.685 0.6843 -15.22 -0.0101 -0.009539 0.006235 | -1.0824
1.685 0.6843 -15.22 -0.0101 -0.009539 0.006235 | -1.0824
1.685 0.6843 -15.22 -0.0101 -0.009539 0.006235 | -1.0824
iteration 6...
1.685 0.6843 -15.22 -0.0101 -0.009539 0.006235 | -1.0824
1.685 0.6843 -15.22 -0.0101 -0.009539 0.006235 | -1.0824
1.685 0.6843 -15.22 -0.0101 -0.009539 0.006235 | -1.0824
1.685 0.6843 -15.22 -0.01008 -0.009539 0.006235 | -1.0824
1.685 0.6843 -15.22 -0.01008 -0.009539 0.006235 | -1.0824
1.685 0.6843 -15.22 -0.01008 -0.009539 0.006235 | -1.0824
iteration 1...
1.633 0.6843 -15.22 -0.01008 -0.009539 0.006235 | -1.082
1.633 0.7622 -15.22 -0.01008 -0.009539 0.006235 | -1.082
1.633 0.7622 -15.34 -0.01008 -0.009539 0.006235 | -1.0821
1.633 0.7622 -15.34 -0.008081 -0.009539 0.006235 | -1.0821
1.633 0.7622 -15.34 -0.008081 -0.006628 0.006235 | -1.0821
1.633 0.7622 -15.34 -0.008081 -0.006628 0.006235 | -1.0821
iteration 2...
1.676 0.7622 -15.34 -0.008081 -0.006628 0.006235 | -1.0821
1.676 0.8166 -15.34 -0.008081 -0.006628 0.006235 | -1.0821
1.676 0.8166 -15.26 -0.008081 -0.006628 0.006235 | -1.0821
1.676 0.8166 -15.26 -0.007103 -0.006628 0.006235 | -1.0821
1.676 0.8166 -15.26 -0.007103 -0.006628 0.006235 | -1.0821
1.676 0.8166 -15.26 -0.007103 -0.006628 0.005891 | -1.0821
iteration 3...
1.676 0.8166 -15.26 -0.007103 -0.006628 0.005891 | -1.0821
1.676 0.8256 -15.26 -0.007103 -0.006628 0.005891 | -1.0821
1.676 0.8256 -15.26 -0.007103 -0.006628 0.005891 | -1.0821
1.676 0.8256 -15.26 -0.006855 -0.006628 0.005891 | -1.0821
1.676 0.8256 -15.26 -0.006855 -0.006628 0.005891 | -1.0821
1.676 0.8256 -15.26 -0.006855 -0.006628 0.005891 | -1.0821
Done 'Coregister: Estimate'
Done

BST> Emptying temporary directory...

with the following messages first ba warning then an error:

BST> Emptying temporary directory...
Warning: NARGCHK will be removed in a future release. Use NARGINCHK or NARGOUTCHK instead.

In xml_parser (line 114)
In xmltree (line 52)
In read_gifti_file (line 15)
In gifti (line 68)
In ImaGIN_spm_eeg_inv_mesh (line 59)
In process_generate_canonical>Compute (line 153)
In process_generate_canonical>ComputeInteractive (line 210)
In process_generate_canonical (line 28)
In scenario_epilepto>ValidateImportAnatomy (line 403)
In scenario_epilepto>@(c)ValidateImportAnatomy() (line 109)
In panel_guidelines>SwitchPanel (line 116)
In panel_guidelines>@(h,ev)SwitchPanel('next') (line 56)

and then the following error messages appear:

Error using read_gifti_file (line 17)
[GIFTI] Loading of XML file C:\brainstorm3\external\ImaGIN\private\SEEG_cortex_hip_amy_8196.surf.gii failed.

Error in gifti (line 68)
this = read_gifti_file(varargin{1},giftistruct);

Error in ImaGIN_spm_eeg_inv_mesh (line 59)
mesh.tess_mni = export(gifti(filename), 'spm');

Error in process_generate_canonical>Compute (line 153)
spmMesh = ImaGIN_spm_eeg_inv_mesh(NiiFile, Resolution);

Error in process_generate_canonical>ComputeInteractive (line 210)
[isOk, errMsg] = Compute(iSubject, iAnatomy, Resolution, 1);

Error in process_generate_canonical (line 28)
eval(macro_method);

Error in scenario_epilepto>ValidateImportAnatomy (line 403)
process_generate_canonical('ComputeInteractive', iSubject, 1, SurfResolution);

Error in scenario_epilepto>@(c)ValidateImportAnatomy() (line 109)
ctrl.fcnValidate{i} = @(c)ValidateImportAnatomy();

Error in panel_guidelines>SwitchPanel (line 116)
[isValidated, errMsg] = ctrl.fcnValidate{iPanel}();

Error in panel_guidelines>@(h,ev)SwitchPanel('next') (line 56)
ctrl.jButtonNext = gui_component('button', jPanelControl, 'br', '>>', buttonFormat, , @(h,ev)SwitchPanel('next'));

SPM8 in installed and under path.

Any ideas?

Many thanks and apologies for the lenghty email.

Stefano Seri

2

Hello

The difference in behavior between the two approaches depends on the default options:

  • when running manually the computation of the "SPM canonical surfaces", it uses the highest resolution available in SPM (20484 vertices)
  • when using the panel "Guidelines > Epileptogenicity maps", it uses by default a modified version of this surface to replicate the results presented in David's article (https://www.ncbi.nlm.nih.gov/pubmed/21975587)

I fixed this discrepancy, now it will be using the default SPM surface everywhere. It will have the same effect of you changing the selected surface (Step #2) to "20484V". After you update Brainstorm, it will select this option by default.

Now, why you were getting this error, this is a mystery. Could you please enter the following lines in your Matlab command window (after starting Brainstorm and running the computation of something involving SPM), and copy-paste the output here:

gifti('C:\brainstorm3\external\ImaGIN\private\SEEG_cortex_hip_amy_8196.surf.gii')
export(gifti('C:\brainstorm3\external\ImaGIN\private\SEEG_cortex_hip_amy_8196.surf.gii'), 'spm');

Thanks
Francois