Correcting Volume Conductor Segmentations - Revision history

Jaehyun at 15:47, 4 March 2024

2024-03-04T15:47:11Z

Robert at 09:09, 5 May 2021

2021-05-05T09:09:39Z

Jaehyun: /* Modifying the Mask in A Third-party Tool */

2018-08-09T19:28:48Z

‎Modifying the Mask in A Third-party Tool

Jaehyun: /* Exporting the Data Files from BESA MRI */

2018-08-02T08:41:54Z

‎Exporting the Data Files from BESA MRI

Jaehyun: /* Exporting the Data Files from BESA MRI */

2018-07-19T13:45:02Z

‎Exporting the Data Files from BESA MRI

Jaehyun: /* Using the Modified Segmentation Mask in BESA MRI */

2018-07-19T13:39:14Z

‎Using the Modified Segmentation Mask in BESA MRI

Jaehyun: /* Exporting the Data Files from BESA MRI */

2018-07-19T13:37:19Z

‎Exporting the Data Files from BESA MRI

Jaehyun: /* Modifying the Mask in A Third-party Tool */

2017-05-18T09:17:08Z

‎Modifying the Mask in A Third-party Tool

Benjamin: /* Modifying the Mask in A Third-party Tool */

2016-06-17T10:20:49Z

‎Modifying the Mask in A Third-party Tool

Benjamin: /* Using the Modified Segmentation Mask in BESA MRI */

2016-06-17T10:17:36Z

‎Using the Modified Segmentation Mask in BESA MRI

@@ Line 2: / Line 2: @@
 |title = Module information
 |module = BESA MRI
-|version = BESA MRI 2.0 or higher
+|version = BESA MRI 2.0
 }}

@@ Line 2: / Line 2: @@
 |title = Module information
 |module = BESA MRI
-|version = 2.0 or higher
+|version = BESA MRI 2.0 or higher
 }}

@@ Line 47: / Line 47: @@
 == Modifying the Mask in A Third-party Tool ==
-There are several third-party tools available which are able to read the data from Analyze format, and which allow to manually correct the segmentation mask. Here, as an example it will be described how [https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslView FslView] can be used to correct the mask.
+There are several third-party tools available which are able to read the data from Analyze format, and which allow to manually correct the segmentation mask (e.g., [https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslView FslView] and [http://www.itksnap.org/pmwiki/pmwiki.php ITK-SNAP]).
-* Start ''FslView''.
+Here, as an example it will be described how [https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslView FslView] can be used to correct the mask.
 * Load the T1-weighted MRI and optionally the T2-weighted MRI.
 * Load the volume conductor segmentation mask.
@@ Line 65: / Line 67: @@
 * This means, if you want to mark some voxels as skull set the ''Pen Value'' in the tool bar to 3 and paint the voxels in the displayed mask.
 * For comparison with the underlying MRI the opacity of the mask can be changed using the slider in the selection window.
-* After you have finished modifying the segmentation mask save it using the ''File -> Save as ...'' command.
+* After you have finished modifying the segmentation mask save it using the ''File &rarr; Save as ...'' command.
-'''Please, make sure, that the saved mask is still correctly oriented, especially, with regard to a potential left-right flip.'''
+'''Please make sure that the saved mask is still correctly oriented, especially, with regard to a potential left-right flip.'''
-'''In addition, ascertain that the image parameters (dimensions, voxels size) are exactly the same in the modified, saved image header as in the original image header. If this is not the case then BESA MRI will ignore the modified segmentation.'''
+'''In addition, ascertain that the image parameters (dimensions and voxels size) are exactly the same in the modified, saved image header as in the original image header. If this is not the case then BESA MRI will ignore the modified segmentation.'''
 == Using the Modified Segmentation Mask in BESA MRI ==

@@ Line 38: / Line 38: @@
 * Open a segmentation project in BESA MRI and run the volume conductor segmentation. If the project was already finished press the '''Modify''' button to re-load the project data.
 * After the volume conductor segmentation has finished the segmentation mask, a copy of the T1-weighted image and, if available, a copy of the T2-weighted image are written to the temporary project folder.
-* Save the project to store the data to the BESA MRI project data folder.
+* '''Save the project''' to store the data to the BESA MRI project data folder.
 * The user accessible image files and masks can now be found in the following subfolders of your project folder:
-** <tt>MRIFiles\VMRFiles\<Project name>_VCS_WS.hdr</tt>
+** <tt>\MRIFiles\VMRFiles\<Project name>_VCS_WS.hdr</tt>
-** <tt>MRIFiles\VMRFiles\<Project name>_T1_WS.hdr</tt>
+** <tt>\MRIFiles\VMRFiles\<Project name>_T1_WS.hdr</tt>
-** <tt>MRIFiles\VMRFiles\<Project name>_T2_WS.hdr</tt>
+** <tt>\MRIFiles\VMRFiles\<Project name>_T2_WS.hdr</tt>
 * For each of the files ending on '''.hdr''' you will also find an '''.img''' file to complete the Analyze image.

@@ Line 36: / Line 36: @@
 * Switch on the output of the user accessible image files and segmentation masks. To do this, using any text editor open the project file which is located in the project data folder under <tt>'''\MRIFiles\ProjectFiles\<Project name>.seg'''</tt>. Find the line starting with <tt>'''UseUserModSegm'''</tt> in the <tt>'''[VolCondSegm]'''</tt> section. Modify the line so that it says '''<tt>UseUserModSegm=1</tt>'''. If the line does not exist add it to project file.
-* Open a segmentation project in BESA MRI and run the volume conductor segmentation. If the project was already finished press the ''Modify'' button to re-load the project data.
+* Open a segmentation project in BESA MRI and run the volume conductor segmentation. If the project was already finished press the '''Modify''' button to re-load the project data.
 * After the volume conductor segmentation has finished the segmentation mask, a copy of the T1-weighted image and, if available, a copy of the T2-weighted image are written to the temporary project folder.
 * Save the project to store the data to the BESA MRI project data folder.

@@ Line 72: / Line 72: @@
 == Using the Modified Segmentation Mask in BESA MRI ==
 After saving the mask copy it back to the project folder where the original segmentation was written (i.e.,
-<tt>MRIFiles\VMRFiles\<Project name>_VCS_WS.hdr</tt>). Please note, that both, the ''*.hdr'' and the ''*.img'' file,
+'''<tt>MRIFiles\VMRFiles\<Project name>_VCS_WS.hdr</tt>'''). Please note, that both, the '''*.hdr''' and the '''*.img''' file,
 have to be copied.
 Next, start BESA MRI and again open the segmentation project associated with the corrected mask. If the
-segmentation project has been finalized before, press the ''Modify'' button to re-load the project data.
+segmentation project has been finalized before, press the '''Modify''' button to re-load the project data.
 Now during the volume conductor workstep the manually corrected segmentation mask will be read. It
 replaces the original automatically computed segmentation mask, and the modified mask will be used in
@@ Line 84: / Line 85: @@
 After finalization save the project. This will also save the manually corrected segmentation mask as the
-segmentation mask that was used for this project. The FE mesh and source space information now based
+segmentation mask that was used for this project. The ''FE mesh'' and ''source space information'' now based
 on the manually corrected segmentation can finally be used in a coregistration project to compute the
 individual FEM leadfield.
 [[Category:MRI]]