From 48efa98ddadb2a95f22dc3116cf7dbd6d3b3aaaf Mon Sep 17 00:00:00 2001 From: Samuel St-Jean Date: Tue, 5 Jan 2016 15:14:10 +0100 Subject: [PATCH 1/2] DOC: Fixed typo --- nibabel/trackvis.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nibabel/trackvis.py b/nibabel/trackvis.py index a76baaff75..6d9d12137f 100644 --- a/nibabel/trackvis.py +++ b/nibabel/trackvis.py @@ -47,7 +47,7 @@ ('hdr_size', 'i4'), ] -# Version 2 adds a 4x4 matrix giving the affine transformtation going +# Version 2 adds a 4x4 matrix giving the affine transformation going # from voxel coordinates in the referenced 3D voxel matrix, to xyz # coordinates (axes L->R, P->A, I->S). IF (0 based) value [3, 3] from # this matrix is 0, this means the matrix is not recorded. From 12c61956bc2529906990832d34c714c8d82b97de Mon Sep 17 00:00:00 2001 From: Samuel St-Jean Date: Tue, 5 Jan 2016 15:55:51 +0100 Subject: [PATCH 2/2] more typo fixing --- nibabel/trackvis.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nibabel/trackvis.py b/nibabel/trackvis.py index 6d9d12137f..541ff17985 100644 --- a/nibabel/trackvis.py +++ b/nibabel/trackvis.py @@ -111,7 +111,7 @@ def read(fileobj, as_generator=False, points_space=None, strict=True): The coordinates in which you want the points in the *output* streamlines expressed. If None, then return the points exactly as they are stored in the trackvis file. The points will probably be in - trackviz voxmm space - see Notes for ``write`` function. If 'voxel', + trackvis voxmm space - see Notes for ``write`` function. If 'voxel', we convert the points to voxel space simply by dividing by the recorded voxel size. If 'rasmm' we'll convert the points to RAS mm space (real space). For 'rasmm' we check if the affine is set and matches the voxel @@ -291,8 +291,8 @@ def write(fileobj, streamlines, hdr_mapping=None, endianness=None, points_space : {None, 'voxel', 'rasmm'}, optional The coordinates in which the points in the input streamlines are expressed. If None, then assume the points are as you want them - (probably trackviz voxmm space - see Notes). If 'voxel', the points - are in voxel space, and we will transform them to trackviz voxmm space. + (probably trackvis voxmm space - see Notes). If 'voxel', the points + are in voxel space, and we will transform them to trackvis voxmm space. If 'rasmm' the points are in RAS mm space (real space). We transform them to trackvis voxmm space. If 'voxel' or 'rasmm' we insist that the voxel sizes and ordering are set to non-default values. If 'rasmm' we @@ -331,7 +331,7 @@ def write(fileobj, streamlines, hdr_mapping=None, endianness=None, Notes ----- Trackvis (the application) expects the ``points`` in the streamlines be in - what we call *trackviz voxmm* coordinates. If we have a point (x, y, z) in + what we call *trackvis voxmm* coordinates. If we have a point (x, y, z) in voxmm coordinates, and ``voxel_size`` has the voxel sizes for each of the 3 dimensions, then x, y, z refer to mm in voxel space. Thus if i, j, k is a point in voxel coordinates, then ``x = i * voxel_size[0]; y = j * @@ -343,7 +343,7 @@ def write(fileobj, streamlines, hdr_mapping=None, endianness=None, axis goes from posterior to anterior, "S" -> inferior to superior. If "voxel_order" is empty we assume "LPS". - This information comes from some helpful replies on the trackviz forum + This information comes from some helpful replies on the trackvis forum about `interpreting point coordiantes `_ '''