DWIConvert Training Resources - Revision history

Spujol: /* Conversion from the Command Line */

2014-07-03T19:29:17Z

Conversion from the Command Line

Spujol: /* Conversion from the Command Line */

2014-07-03T19:26:30Z

Conversion from the Command Line

Spujol at 19:17, 3 July 2014

2014-07-03T19:17:13Z

Spujol at 19:16, 3 July 2014

2014-07-03T19:16:48Z

Farukhk at 18:28, 25 June 2014

2014-06-25T18:28:23Z

Farukhk at 16:16, 20 June 2014

2014-06-20T16:16:35Z

Farukhk at 18:49, 18 June 2014

2014-06-18T18:49:58Z

Farukhk at 16:21, 18 June 2014

2014-06-18T16:21:07Z

Farukhk at 16:18, 18 June 2014

2014-06-18T16:18:39Z

Farukhk at 16:11, 18 June 2014

2014-06-18T16:11:45Z

← Older revision		Revision as of 19:29, 3 July 2014
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	==Conversion from the Command Line==		==Conversion from the Command Line==

−	/Applications/Slicer.app/Contents/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/EAAG_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/EAAG_vtkMRMLDiffusionWeightedVolumeNodeC.nrrd --inputDicomDirectory . --outputBValues bval --outputBVectors bvec --outputDirectory . --smallGradientThreshold 0.2	+	*Slicer build
		+	NrrdToFSL: /Applications/Slicer.app/Contents/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/EAAG_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/EAAG_vtkMRMLDiffusionWeightedVolumeNodeC.nrrd --inputDicomDirectory . --outputBValues bval --outputBVectors bvec --outputDirectory . --smallGradientThreshold 0.2
		+
		+	*Slicer executable
		+	NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ~/Desktop/test/dwi1.nhdr --outputVolume ~/Desktop/test/dwi1_fsl.nii.gz --outputBValues ~/Desktop/test/bvals.txt --outputBVectors ~/Desktop/test/bvec.txt FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ~/Desktop/test/dwi1_fsl.nii.gz --outputVolume ~/Desktop/test/dwi1_reconverted.nrrd --inputBValues ~/Desktop/test/bvals.txt --inputBVectors ~/Desktop/test/bvec.txt

← Older revision		Revision as of 19:26, 3 July 2014
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	==Conversion from the Command Line==		==Conversion from the Command Line==
		+
		+	/Applications/Slicer.app/Contents/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/EAAG_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd --outputVolume /var/folders/7k/pwsk6_bd2tg9g58l7j_2d3cr0000gn/T/Slicer/EAAG_vtkMRMLDiffusionWeightedVolumeNodeC.nrrd --inputDicomDirectory . --outputBValues bval --outputBVectors bvec --outputDirectory . --smallGradientThreshold 0.2

← Older revision		Revision as of 19:17, 3 July 2014
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	4. Nifti is a revised version of the Analyze format where the header and pixel data are usually merged into a single ".nii" file. The Nifti format stores the orientation of the image volume in two ways: one, using both the rotation and translation in order to map the voxel coordinates to the specific scanner's frame of reference, the second method saves the general linear transformation to change the alignment of the image volume to a more standard coordinate system. (Larobina M, Murino L: Medical Image File Formats. J Digit Imaging (2014) 27:200-206)		4. Nifti is a revised version of the Analyze format where the header and pixel data are usually merged into a single ".nii" file. The Nifti format stores the orientation of the image volume in two ways: one, using both the rotation and translation in order to map the voxel coordinates to the specific scanner's frame of reference, the second method saves the general linear transformation to change the alignment of the image volume to a more standard coordinate system. (Larobina M, Murino L: Medical Image File Formats. J Digit Imaging (2014) 27:200-206)
		+
		+	==Conversion from the Command Line==

@@ Line 3: / Line 3: @@
 [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DWIConverter DWIConverter Documentation]
-Parameters of the Slicer4.3.1 version
+==Parameters of the Slicer4.3.1 version==
 *Conversion Options: Options used in all modes

@@ Line 3: / Line 3: @@
 [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DWIConverter DWIConverter Documentation]
-Parameters of the Slicer4.3 version
+Parameters of the Slicer4.3.1 version
-*Common Parameters: Parameters used in all modes
+*Conversion Options: Options used in all modes
 *Input DWI volume file (inputVolume): Input DWI volume -- not used for DicomToNrrd mode.
 *Output Filename (outputVolume): Output filename (.nhdr or .nrrd)
-*Output fMRI file (fMRIOutput): Output a NRRD file, but without gradients
+*Dicom To NiftiNrrd Conversion: Parameters for Dicom to NRRD Conversion
 *Input Dicom Data (inputDicomDirectory): Directory holding Dicom series
 *Output Directory (outputDirectory): Directory holding the output NRRD file
 *Gradient Vector File (gradientVectorFile): Text file giving gradient vectors
 *Small Gradient Threshold (smallGradientThreshold): If a gradient magnitude is greater than 0 and less than smallGradientThreshold, then *DWIConvert will display an error message and quit, unless the useBMatrixGradientDirections option is set.
@@ Line 18: / Line 25: @@
 *Use Identity Measurement Frame (useIdentityMeaseurementFrame): Adjust all the gradients so that the measurement frame is an identity matrix.
 *Use BMatrix Gradient Directions (useBMatrixGradientDirections): Fill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data. In some cases the standard public gradients are not properly computed. The gradients can emperically computed from the private BMatrix fields. In some cases the private BMatrix is consistent with the public grandients, but not in all cases, when it exists BMatrix is usually most robust.

← Older revision		Revision as of 16:16, 20 June 2014
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	3. ‹fMRIOutput ‹ this outputs a NRRD file, but doesn¹t include gradient vectors. It would be used if you were interested in converting functional MRI datasets, instead of DWI datasets.		3. ‹fMRIOutput ‹ this outputs a NRRD file, but doesn¹t include gradient vectors. It would be used if you were interested in converting functional MRI datasets, instead of DWI datasets.

−	4. ~~NIfTi-FSL~~ is ~~FSL that supports input and output~~ of ~~NIfTI files. It can read both compressed~~ and ~~uncompressed image files with one of the following extensions:~~ .nii .~~nii.gz .hdr .hdr.gz .img .img.gz~~	+	4. Nifti is a revised version of the Analyze format where the header and pixel data are usually merged into a single ".nii" file. The Nifti format stores the orientation of the image volume in two ways: one, using both the rotation and translation in order to map the voxel coordinates to the specific scanner's frame of reference, the second method saves the general linear transformation to change the alignment of the image volume to a more standard coordinate system. (Larobina M, Murino L: Medical Image File Formats. J Digit Imaging (2014) 27:200-206)
−	~~FSL command lines accept a basename without extensions but it is best to avoid "multiple files~~ in ~~different formats that share~~ the ~~same extension" since~~ the ~~program tends~~ to ~~terminate in these cases.~~
−	~~FSLView images can be rotated~~ to ~~match~~ the ~~avg152~~ standard ~~images which has a right-handed~~ coordinate system. ~~For more information visit http~~:~~//nifti.nimh.nih.gov~~.

← Older revision		Revision as of 18:49, 18 June 2014
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	3. ‹fMRIOutput ‹ this outputs a NRRD file, but doesn¹t include gradient vectors. It would be used if you were interested in converting functional MRI datasets, instead of DWI datasets.		3. ‹fMRIOutput ‹ this outputs a NRRD file, but doesn¹t include gradient vectors. It would be used if you were interested in converting functional MRI datasets, instead of DWI datasets.
		+
		+	4. NIfTi-FSL is FSL that supports input and output of NIfTI files. It can read both compressed and uncompressed image files with one of the following extensions: .nii .nii.gz .hdr .hdr.gz .img .img.gz
		+	FSL command lines accept a basename without extensions but it is best to avoid "multiple files in different formats that share the same extension" since the program tends to terminate in these cases.
		+	FSLView images can be rotated to match the avg152 standard images which has a right-handed coordinate system. For more information visit http://nifti.nimh.nih.gov.

@@ Line 41: / Line 41: @@
 ‹useBMatrixGradientDirections
-  From DWIConvert ‹help output: Fill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data. In some cases the standard public gradients are not properly computed.  The gradients can empirically computed from the private BMatrix fields.  In some cases the private BMatrix is consistent with the public grandients, but not in all cases, when it exists BMatrix is usually most robust.
+From DWIConvert ‹help output: Fill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data. In some cases the standard public gradients are not properly computed.  The gradients can empirically computed from the private BMatrix fields.  In some cases the private BMatrix is consistent with the public grandients, but not in all cases, when it exists BMatrix is usually most robust.
 In other words, the Siemens data includes both a Bmatrix tag, and an explicit set of gradient vectors. For some DWI datasets, the scanner puts

← Older revision		Revision as of 16:11, 18 June 2014
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	*B Vector File (outputBVectors): B Vector text file		*B Vector File (outputBVectors): B Vector text file

		+
		+	Description of different sections:
		+
		+	1. Output OPtions:

	‹writeProtocolGradientsFile ‹ writes the DWI gradient vectors as a simple		‹writeProtocolGradientsFile ‹ writes the DWI gradient vectors as a simple