Documentation/4.8/Modules/GeodesicSlicer - Revision history

Frederic at 18:12, 7 January 2019

2019-01-07T18:12:19Z

Frederic at 18:16, 23 October 2018

2018-10-23T18:16:16Z

Frederic at 16:11, 6 August 2018

2018-08-06T16:11:12Z

Frederic at 15:28, 31 July 2018

2018-07-31T15:28:12Z

Frederic at 12:01, 30 July 2018

2018-07-30T12:01:51Z

Frederic at 09:57, 5 July 2018

2018-07-05T09:57:46Z

Frederic at 13:34, 31 May 2018

2018-05-31T13:34:49Z

Frederic: /* rTMS resting motor threshold- Correction factor */

2018-05-28T15:15:24Z

rTMS resting motor threshold- Correction factor

Frederic at 15:14, 28 May 2018

2018-05-28T15:14:26Z

Frederic at 15:13, 28 May 2018

2018-05-28T15:13:40Z

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 * Dr. Andras Lasso, Ph.D., Queen's University.
-''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Schizophrenia Bulletin, submitted</ref>.''
+''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''
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 * Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
 * Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
 * Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
 * Dr. Csaba Pinter, MSc, Queen's University.

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 *'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.
 *'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref>
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 A typical straightforward Geodesic Slicer workflow for consists of the following steps:
-# Load a volume.nii.
+# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
 # Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
 # Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).

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 * Dr. Andras Lasso, Ph.D., Queen's University.
-''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Biological Psychiatry, submitted</ref>.''
+''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Schizophrenia Bulletin, submitted</ref>.''
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 # Load a volume.nii.
 # Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
-# Press the button "Create a mesh".
+# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
 #*Wait a moment.
 #Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

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 # Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
 #* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1.
-#* 1/ The first according to Stokes et al. Clin  Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7 x (SCDx - SCDm) + rMT]
+#* 1/ The first according to Stokes et al. Clin  Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT]
-#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDt-SCDm)]
+#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)]
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 *'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
 # Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.
-# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.
+# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
 #* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
 #* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.

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 The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make  10-20 system.  This module can be used for:
 *Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
-*Surgery measurement
+*Surgery measurement.
-*3D printing
+*3D printing.
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