diff --git a/docs/assets/figures/opm/coreg_new.png b/docs/assets/figures/opm/coreg_new.png new file mode 100644 index 0000000..3429f13 Binary files /dev/null and b/docs/assets/figures/opm/coreg_new.png differ diff --git a/docs/assets/figures/opm/coreg_template_new.PNG b/docs/assets/figures/opm/coreg_template_new.PNG new file mode 100644 index 0000000..344c9da Binary files /dev/null and b/docs/assets/figures/opm/coreg_template_new.PNG differ diff --git a/docs/assets/figures/opm/sourse_evoked_t_new.png b/docs/assets/figures/opm/sourse_evoked_t_new.png new file mode 100644 index 0000000..b86d917 Binary files /dev/null and b/docs/assets/figures/opm/sourse_evoked_t_new.png differ diff --git a/docs/tutorials/opm/evoked_source/index.md b/docs/tutorials/opm/evoked_source/index.md index 295c8a1..9b44c7e 100644 --- a/docs/tutorials/opm/evoked_source/index.md +++ b/docs/tutorials/opm/evoked_source/index.md @@ -59,16 +59,17 @@ When we do not have an MRI for a participant we can register the MNI template sc
- +
Before we run the coregistration code we need to mark a number of fiducial points on our meshes. We will need to mark -1. 3 points on the helmet file (`S.helmetref`). -2. 3 corresponding points on the mesh with the head and helmet present (`S.headhelmetref`). -3. 3 points on the head shape mesh (`S.headfid`). -4. 3 point on the corresponding mesh file with the head and helmet present (`S.headhelmetfid`). +1. 3 points on the helmet file (`S.helmetref1`). +2. 3 corresponding points on the mesh with the head and helmet present (`S.headhelmetref1`). +3. 3 points on the head shape mesh (`S.headref2`). +4. 3 point on the corresponding mesh file with the head and helmet present (`S.headhelmetref2`). +5. 3 fiducial points, should be in order nas - lpa - rpa (`S.fiducials`). To mark these points we can use [`spm_mesh_selct`](https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/opm/coreg/#manually-marking-fiducials-on-meshes). @@ -79,32 +80,37 @@ S = []; S.D = eD; S.headfile = 'head.obj'; - S.helmetref = ... -[0,133.9,-24;... %point 1 --114,30.5,-61;... %point 2 -116,29,-59]; %point 3 + S.helmetref1 = ... +[0,133.9,-24;... % point 1 +-114,30.5,-61;... % point 2 +116,29,-59]; % point 3 -S.headhelmetref = ... -[77,-23,608;... %point 1 -31,90,715;... %point 2 -26,-141,692]; %point 3 +S.headhelmetref2 = ... +[77,-23,608;... % point 1 +31,90,715;... % point 2 +26,-141,692]; % point 3 -S.headfid = ... +S.headref2 = ... +[105, -60, 530.6;... % point 4 +120.2, -10, 503.8;... % point 5 +122.3, 44.7, 533.5]; % point 6 + +S.headhelmetref2 = ... +[29.8, -66.5, 670.6;... % point 4 +40.8, -19.4, 653.9;... % point 5 +37.7, 32.7, 689]; % point 6 + +S.fiducials = ... [111.626,-9,504;... % nas 97, 54, 551;... % lpa -84, -67, 548]; % rpa - -S.headhelmetfid = ... -[33,-22.6,654;... % nas -14.7, 38.9, 699;... % lpa -5,-82,693]; %rpa +84, -67, 548]; % rpa cD = spm_opm_opreg(S); ```
- +
Template Coregistration
@@ -170,7 +176,7 @@ The output, by default, is in MNI space and you can now view the result in your
- +
Source level evoked response
@@ -229,33 +235,39 @@ S = []; S.D = eD; S.headfile = 'head.obj'; - S.helmetref = ... -[0,133.9,-24;... %nas --114,30.5,-61;... %lpa -116,29,-59]; %rpa + S.helmetref1 = ... +[0,133.9,-24;... % point 1 +-114,30.5,-61;... % point 2 +116,29,-59]; % point 3 + +S.headhelmetref2 = ... +[77,-23,608;... % point 1 +31,90,715;... % point 2 +26,-141,692]; % point 3 -S.headhelmetref = ... -[77,-23,608;... %nas -31,90,715;... %lpa -26,-141,692]; %rpa +S.headref2 = ... +[105, -60, 530.6;... % point 4 +120.2, -10, 503.8;... % point 5 +122.3, 44.7, 533.5]; % point 6 -S.headfid = ... +S.headhelmetref2 = ... +[29.8, -66.5, 670.6;... % point 4 +40.8, -19.4, 653.9;... % point 5 +37.7, 32.7, 689]; % point 6 + +S.fiducials = ... [111.626,-9,504;... % nas -97, 54, 551;...% lpa -84, -67, 548]; % rpa +97, 54, 551;... % lpa +84, -67, 548]; % rpa -S.headhelmetfid = ... -[33,-22.6,654;... % nas -14.7, 38.9, 699;...% lpa -5,-82,693]; %rpa -eD = spm_opm_opreg(S); +cD = spm_opm_opreg(S); % daiss data setup %-------------------------------------------------------------------------- bfDir = 'C:\Users\path\to\folder'; S = []; -S.D = fname(eD); +S.D = fname(cD); S.dir = bfDir; S.space = 'Head'; [BF] = bf_wizard_data(S); @@ -295,4 +307,3 @@ bf_stat_evoked_t(S); ``` --8<-- "addons/abbreviations.md" -s \ No newline at end of file