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