2008 Engineering review at Utah:FollowUp - Revision history

Taox: /* DICOM to NRRD converter */

2008-04-03T20:03:11Z

DICOM to NRRD converter

Taox: /* DICOM to NRRD converter */

2008-04-03T20:01:26Z

DICOM to NRRD converter

Taox: /* DICOM to NRRD converter */

2008-04-03T19:29:41Z

DICOM to NRRD converter

Taox: /* DICOM to NRRD converter */

2008-04-03T19:17:37Z

DICOM to NRRD converter

Taox: /* DICOM to NRRD converter */

2008-04-03T19:17:25Z

DICOM to NRRD converter

Taox: /* DICOM to NRRD converter */

2008-04-03T19:13:57Z

DICOM to NRRD converter

Taox: /* DICOM to NRRD converter */

2008-04-03T18:50:30Z

DICOM to NRRD converter

Taox: New page: == DWI Analysis == === DICOM to NRRD converter === === Preprocessing/Correction of Artifacts === === Automatic Population-Based DTI === == Segmentation == === Brain stripping & bias c...

2008-04-03T18:36:40Z

New page: == DWI Analysis == === DICOM to NRRD converter === === Preprocessing/Correction of Artifacts === === Automatic Population-Based DTI === == Segmentation == === Brain stripping & bias c...

New page

== DWI Analysis ==

=== DICOM to NRRD converter ===

=== Preprocessing/Correction of Artifacts ===

=== Automatic Population-Based DTI ===

== Segmentation ==

=== Brain stripping & bias correction ===

=== Brain white matter mask ===

=== Full brain tissue classification ===

=== Automatic brain tissue and lesion analysis ===

== Shape Analysis ==

=== Pipeline for statistical group analysis of populations of shapes ===

@@ Line 8: / Line 8: @@
 The gradient directions from dicom headers and those from the nrrd header generated at Utah differ. These vectors are not related by a rigid transform. In fact, most of them (20 out of 25) are very close, differ by less than 2.5 degrees (0.77+/-0.47 degrees). [The angle between vectors [0.84 0.54] and [0.83 0.55] is about 0.8 degrees.] The other five directions differ by about 40 degrees.
 {|
@@ Line 15: / Line 17: @@
 ! [[Image:Tensor_recon_from_DICOM.png|thumb|300px|Tensor reconstruction results using information from DICOM header]]
 |}
 The space direction and measurement frame in the Utah nrrd header are

@@ Line 12: / Line 12: @@
 |- valign="top"
 ! [[Image:Gradient_Vector_Difference_Dicom_Utah_Nrrd.png|thumb|300px|Difference in gradient directions between Dicom and Utah Nrrd]]
-! [[Image:B_Value_Difference_Dicom_Utah_Nrrd.png|thumb|300px|Difference in b values between Dicom and Utah Nrrd]]
+! [[Image:B_Value_Difference_Dicom_Utah_Nrrd.png|thumb|300px|B values from Utah Nrrd (blue) and Dicom (red)]]
 ! [[Image:Tensor_recon_from_DICOM.png|thumb|300px|Tensor reconstruction results using information from DICOM header]]
 |}

@@ Line 12: / Line 12: @@
 |- valign="top"
 ! [[Image:Gradient_Vector_Difference_Dicom_Utah_Nrrd.png|thumb|300px|Difference in gradient directions between Dicom and Utah Nrrd]]
 ! [[Image:Tensor_recon_from_DICOM.png|thumb|300px|Tensor reconstruction results using information from DICOM header]]
 |}

@@ Line 14: / Line 14: @@
 ! [[Image:Tensor_recon_from_DICOM.png|thumb|300px|Tensor reconstruction results using information from DICOM header]]
 |}
 The B_values normalized by the largest B_value from dicom header and from Utah nrrd header are close, but not identical. In the Utah nrrd header, the B_value was recorded as 1400 (this is supposed to be the largest B_value). But according to the Dicom header, the largest one is 1000. The B_values from dicom range from 50 to 1000 as multiples of 50.

@@ Line 12: / Line 12: @@
 |- valign="top"
 ! [[Image:Gradient_Vector_Difference_Dicom_Utah_Nrrd.png|thumb|300px|Difference in gradient directions between Dicom and Utah Nrrd]]
 |}

← Older revision		Revision as of 19:13, 3 April 2008
Line 8:		Line 8:

	The gradient directions from dicom headers and those from the nrrd header generated at Utah differ. These vectors are not related by a rigid transform. In fact, most of them (20 out of 25) are very close, differ by less than 2.5 degrees (0.77+/-0.47 degrees). [The angle between vectors [0.84 0.54] and [0.83 0.55] is about 0.8 degrees.] The other five directions differ by about 40 degrees.		The gradient directions from dicom headers and those from the nrrd header generated at Utah differ. These vectors are not related by a rigid transform. In fact, most of them (20 out of 25) are very close, differ by less than 2.5 degrees (0.77+/-0.47 degrees). [The angle between vectors [0.84 0.54] and [0.83 0.55] is about 0.8 degrees.] The other five directions differ by about 40 degrees.
		+
		+	{\|
		+	\|- valign="top"
		+	! [[Image:Gradient_Vector_Difference_Dicom_Utah_Nrrd.png\|thumb\|300px\|Difference in gradient directions between Dicom and Utah Nrrd]]
		+	\|}
		+

	The B_values normalized by the largest B_value from dicom header and from Utah nrrd header are close, but not identical. In the Utah nrrd header, the B_value was recorded as 1400 (this is supposed to be the largest B_value). But according to the Dicom header, the largest one is 1000. The B_values from dicom range from 50 to 1000 as multiples of 50.		The B_values normalized by the largest B_value from dicom header and from Utah nrrd header are close, but not identical. In the Utah nrrd header, the B_value was recorded as 1400 (this is supposed to be the largest B_value). But according to the Dicom header, the largest one is 1000. The B_values from dicom range from 50 to 1000 as multiples of 50.

← Older revision		Revision as of 18:50, 3 April 2008
Line 2:		Line 2:

	=== DICOM to NRRD converter ===		=== DICOM to NRRD converter ===
		+
		+	We looked into the diffusion weighted images from Utah acquired on a Siemens scanner. We compared the critical information stored in dicom header and in the nrrd header generated at Utah.
		+
		+	As stated on [[NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI#Private_vendor:_Siemens \| this page]], gradient directions and B_Values are stored in two places in dicom headers. B_values are stored in tag 0019,100c and shadow tag 0029,1010; gradient directions are stored in 0019,100e and 0029,1010. The numbers stored in both places are identical, which means that at minimum, the dicom files are self consistent.
		+
		+	The gradient directions from dicom headers and those from the nrrd header generated at Utah differ. These vectors are not related by a rigid transform. In fact, most of them (20 out of 25) are very close, differ by less than 2.5 degrees (0.77+/-0.47 degrees). [The angle between vectors [0.84 0.54] and [0.83 0.55] is about 0.8 degrees.] The other five directions differ by about 40 degrees.
		+
		+	The B_values normalized by the largest B_value from dicom header and from Utah nrrd header are close, but not identical. In the Utah nrrd header, the B_value was recorded as 1400 (this is supposed to be the largest B_value). But according to the Dicom header, the largest one is 1000. The B_values from dicom range from 50 to 1000 as multiples of 50.
		+
		+	The space direction and measurement frame in the Utah nrrd header are
		+
		+	space directions: (1.97917,0,0) (0,1.97917,0) (0,0,2)
		+	measurement frame: (-1,0,0) (0,1,0) (0,0,1)
		+
		+	while ImageOrientationPatient file in the dicom header is
		+
		+	0.999962, 0.00872651, 0; -0.00872651, 0.999962, 0.
		+
		+	When taking the measurement frame and pixel size (1.9791666 in this case) into consideration, the space direction and measurement frame should be
		+
		+	space directions: (-1.97909,-0.0172712,0) (0.0172712,-1.97909,0) (0,0,2)
		+	measurement frame: (1,0,0) (0,1,0) (0,0,1)

	=== Preprocessing/Correction of Artifacts ===		=== Preprocessing/Correction of Artifacts ===