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Dear Fieldtrip community! </div>
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I aim trying to generate source model for meg data files recorded in Elekta Neuromag system. However, I have generated the Freesurfer files using each subject's T1w MRI, without re-aligning the volume before running Freesurfer as suggested in this tutorial
(sorry I was too used to working in Brainstorm!). </div>
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Now, I am trying to generate a headmodel from the Freesurfer generated T1.mgz using the following code, but I keep getting a warning (also shown below). </div>
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mri_file=strcat(<path to freesurfer dir>, '/mri/T1.mgz'); </div>
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mri=ft_read_mri(mri_file); </div>
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% re-align the volume </div>
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cfg=[]; </div>
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cfg.method='interactive'; </div>
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cfg.coordsys='neuromag'; </div>
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mri=ft_volumerealign(cfg,mri); </div>
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% create seg file </div>
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cfg=[]; </div>
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cfg.output='brain'; </div>
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cfg.brainthreshold=0.5; </div>
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seg=ft_volumesegment(cfg,mri); </div>
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The above code runs, but I am getting the following warning: </div>
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Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND=1.045258e-22. </div>
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My question is: </div>
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<div role="presentation" class="elementToProof">Should I instead use the original T1w MRI for creating the headmodel, and use the Freesurfer T1.mgz of the same subject for creating the same model? </div>
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<div role="presentation" class="elementToProof">If yes, what is the best way to co-register and create source model from a Freesurfer generated T1.mgz from a T1.nii which was not aligned to the neuromag coordsys before recon-all. </div>
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For context my ultimate aim is to generate virtual channels as per the Schaefer's atlas for the entire .fif file; i.e. simply go from the sensor space to roi parcellated source space after cleaning the data (using ICA). </div>
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Any help/suggestions here would be very useful. </div>
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Kind regards, </div>
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Kiran </div>
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