Arithmetic about apply regularization transform

slicer365 · August 23, 2023, 7:07am

I am developing an independent software for my clients.

I need this function to correct the data.

The tilt value can be found in Tag,

but how to make changes to the data,

I searched the source code,

but I can’t find the implementation entry for this.

Can anyone help me? Thank you !

jcfr · August 23, 2023, 12:36pm

I searched the source code,

If you search for the words Regularization and regularization, you should be able to identify the relevant files.

Let us know if you sill have issues.

slicer365 · August 23, 2023, 1:06pm

Here is the result ,it seems that there is no what I want.

pieper · August 23, 2023, 1:54pm

The description and the corresponding source code are here:

github.com/Slicer/Slicer

ENH: model DICOM acquisition geometry (addresses #4409)

committed 12:57PM - 20 Oct 17 UTC

pieper

+278 -6

Add a step to the DICOMScalarVolumePlugin to check that the loaded volume node's… slice geometry matches what is expected from the position and orientation information of the individual slices in the DICOM headers. If needed, a grid transform is created to reposition each slice to the appropriate position in patient space. Use an empirically defined epsilon threshold to decide if an acquisition transform is needed. The selected value of 1e-3 millimeters (one micrometer) is still very small by medical imaging standards but is large enough that rounding errors and other small variations do not result in extra correction transforms when they won't add real value. The error is defined as the max absolute difference in any coordinate of the corner of any slice so it is designed to handle gantry tilt, missing slices, and irregularly spaced slices. The DICOMReaders self test has been extended to test this in the case where slices are missing from the middle of the volume. The grid transform results in an interpolated band of pixels using information from adjacent slices to 'fill in' for the missing data. The test confirms that the last slice of the reconstructed volume is in the expected location in patient space. This correction means that calculations like ruler or segment statistics can be robust even with missing slices. Currently the only available testing data is for the case of missing slices. However this code should allow proper loading and display of several not-uncommon imaging scenarios: 1) Missing slices due to network failure or accidental file deletion. 2) Gantry tilted image acquisitons (see #4409) which is used, for example, to minimize radiation exposure to the retinas especially in pediatric imaging. 3) Variable table speed during CT acquisition, which is sometimes used in abdominal or musculoskeletal imaging to provide high resolution in selected body parts and lower resolution between (e.g. high res at the ankle, knee and hip, but low res in the shin and thigh). Consderations: By creating a transform we preserve the original data and leave it to the user to resample if desired. The option of resampling during load was rejected since it is unclear what sampling grid would be best in all cases. Although the transform should correct the geometry, a warning dialog is still generated during loading since the issue could be correctable (such as missing slices) or may be triggered by other data issues not forseen by this code. Most DICOM data has identical row and column spacing but when they do not it's critical to have the right spacing geomtry. This code uses the correct definitions from the standard. Where PixelSpacing is row/column but ImageOrientationPatient if column/row We check and avoid ValueError warning when dicom files do not have geometry information. svn-url: http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=26500 git-svn-id: http://svn.slicer.org/Slicer4/trunk@26500 3bd1e089-480b-0410-8dfb-8563597acbee

slicer365 · August 23, 2023, 2:23pm

Thank you very much !

jcfr · August 23, 2023, 3:22pm

To complete my previous answer, doing a case-insensitive search returns the following:

$ rg -i regularization

[...]

Docs/user_guide/modules/dicom.md
186:        - Acquisition geometry regularization option supports the creation of a nonlinear transform that corrects for things like missing slices or gantry tilt in the acquisition.  See more information [here](https://github.com/Slicer/Slicer/commit/3328b81211cb2e9ae16a0b49097744171c8c71c0)
243:Scanners may create image volumes with varying image slice spacing. Slicer can represent such images in the scene by apply a non-linear transform. To enable this feature, go to menu: Edit / Application settings / DICOM and set *Acquisition geometry regularization* to *apply regularization transform*. Slice view, segmentation, and many other features work directly on non-linearly transformed volumes. For some other features, such as volume rendering, you need to harden the transform on the volume: go to Data module, in the row of the volume node, right-click on the transform column, and choose *Harden transform*.

Modules/Scripted/DICOMLib/DICOMUtils.py
665:    # Get acquisition geometry regularization setting value
667:    acquisitionGeometryRegularizationEnabled = (settings.value("DICOM/ScalarVolume/AcquisitionGeometryRegularization", "default") != "none")
688:                if acquisitionGeometryRegularizationEnabled:
691:                    warningText += ("  If loaded image appears distorted, enable 'Acquisition geometry regularization'"

Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py
88:                                          " If no regularization is applied then image may appear distorted if it was acquired with irregular geometry.")
90:        importFormatsComboBox.addItem(_("default (apply regularization transform)"), "default")
92:        importFormatsComboBox.addItem(_("apply regularization transform"), "transform")
96:        formLayout.addRow(_("Acquisition geometry regularization:"), importFormatsComboBox)
98:            "DICOM/ScalarVolume/AcquisitionGeometryRegularization", importFormatsComboBox,
137:    def acquisitionGeometryRegularizationEnabled(self):
139:        return (settings.value("DICOM/ScalarVolume/AcquisitionGeometryRegularization", "default") != "none")
542:                                                                addAcquisitionTransformIfNeeded=self.acquisitionGeometryRegularizationEnabled())
850:                    logging.warning(warningText + "  Regularization transform is not added, as the option is disabled.")

[...]

Topic		Replies	Views
Gantry tilt correction in CT DICOMS Support dicom	3	1311	August 31, 2021
Regularization transform is not applied to generated models Support	10	1415	May 30, 2019
How to adjust the distorted image? Support	87	7832	September 8, 2021
Understanding CT Image spacing and Acquisition geometry regularization Support	5	1289	November 13, 2023
Uneven slice thickness Support dicom	11	1522	November 13, 2023

Arithmetic about apply regularization transform

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