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Today

kompan added a comment to T30435: Rename "Time" to "Timestep" in Image Navigator?.

It is not straighforward which name to use, since what is displayed in the Image Navigator depends on if the dynamic image has been globally or locally initiated. Therefore, for now we keep the name "Time" in the Image Navigator. What is shown is therefore not obvious for the user and should be documented clearly in the F1 help. It needs to be checked if this is the case.
A solution could be to provide a separate slider in the ModelFit Inspector View.

Wed, May 8, 11:21 AM · MITK, Next Milestone, Checklist
kompan added projects to T30425: [SEG] Segment Anything - Loading errors occur when opening the preferences: MITK (v2024.06), Checklist.
Wed, May 8, 11:03 AM · Checklist, MITK (v2024.06)
kompan moved T18489: Help perspective cannot be closed from Backlog to Cycle on the MITK (v2024.06) board.
Wed, May 8, 9:57 AM · Request for Discussion, MITK (v2024.06)
kompan reopened T18489: Help perspective cannot be closed as "Open".
Wed, May 8, 9:41 AM · Request for Discussion, MITK (v2024.06)
kompan added a comment to T18489: Help perspective cannot be closed.

Since this issue was pointed out by a user recently (and I also found it confusing before reading this task description), I would like to re-open this task for discussion.

Wed, May 8, 9:40 AM · Request for Discussion, MITK (v2024.06)

Yesterday

kompan triaged T30437: [Perfusion] Provide example start parameter image for checklists as Low priority.
Tue, May 7, 10:49 AM · Checklist, MITK (v2024.06)
kompan triaged T30436: [Perfusion] Checkbox for Start Parameters instead of radio button as Low priority.
Tue, May 7, 10:43 AM · Checklist, MITK (v2024.06)
kompan added a project to T30435: Rename "Time" to "Timestep" in Image Navigator?: Request for Discussion.
Tue, May 7, 10:40 AM · MITK, Next Milestone, Checklist
kompan triaged T30435: Rename "Time" to "Timestep" in Image Navigator? as Normal priority.
Tue, May 7, 9:48 AM · MITK, Next Milestone, Checklist
kompan triaged T30434: [Perfusion] Concentration curve converter VFA box tab key skips flip angles as Normal priority.
Tue, May 7, 9:40 AM · Next Milestone, Checklist, MITK (v2024.06)
kompan triaged T30433: [Perfusion] Inconsistent appearance of info box message "Cannot compute parameters. No node selected." as Normal priority.
Tue, May 7, 9:11 AM · MITK, Next Milestone
kompan updated the task description for T30432: [Perfusion] Possible to write text into info box.
Tue, May 7, 9:03 AM · MITK (v2024.06)
kompan triaged T30432: [Perfusion] Possible to write text into info box as Normal priority.
Tue, May 7, 8:57 AM · MITK (v2024.06)

Mon, May 6

kompan added a comment to T30428: DCE MR Perfusion DataFit View: Selected Mask widget can't find DICOM segmentation nodes.

It seems to be an issue with this specific dataset. I made new set of segmentations (Prostate label and AIF label) and stored them each as DICOM segmentation. And now I find that the segmentation nodes are found as expected. It needs to be determined if the old data set is somehow corrupted or if it is a backwards compatibility issue (the masks were initially created in 2019).

Mon, May 6, 11:10 AM · Checklist, MITK (v2024.06)
kompan added a subtask for T29524: SAM in MITK: T30427: [SEG] No status change message after changing model type to ‘vit_l’..
Mon, May 6, 10:02 AM · MITK
kompan added a parent task for T30427: [SEG] No status change message after changing model type to ‘vit_l’.: T29524: SAM in MITK.
Mon, May 6, 10:02 AM · Checklist, MITK (v2024.06)
kompan triaged T30427: [SEG] No status change message after changing model type to ‘vit_l’. as Normal priority.
Mon, May 6, 10:02 AM · Checklist, MITK (v2024.06)
kompan added a subtask for T29524: SAM in MITK: T30426: [SEG] Highlight importance of level window in Segment Anything.
Mon, May 6, 9:58 AM · MITK
kompan added a parent task for T30426: [SEG] Highlight importance of level window in Segment Anything: T29524: SAM in MITK.
Mon, May 6, 9:58 AM · Checklist, MITK (v2024.06)
kompan triaged T30426: [SEG] Highlight importance of level window in Segment Anything as Normal priority.
Mon, May 6, 9:57 AM · Checklist, MITK (v2024.06)
kompan triaged T30425: [SEG] Segment Anything - Loading errors occur when opening the preferences as Normal priority.
Mon, May 6, 9:54 AM · Checklist, MITK (v2024.06)
kompan updated the task description for T30424: [SEG] Reduce size of dots in Segment Anything.
Mon, May 6, 9:44 AM · Checklist, MITK (v2024.06)
kompan triaged T30424: [SEG] Reduce size of dots in Segment Anything as Normal priority.
Mon, May 6, 9:42 AM · Checklist, MITK (v2024.06)
kompan triaged T30423: [SEG] Segment Anything misleading GPU message for first time users as Normal priority.
Mon, May 6, 9:33 AM · Checklist, MITK (v2024.06)

Wed, May 1

kompan committed rMITKf298153c27b2: Update data selection concept in perfusion/modelfit-related views. (authored by kompan).
Update data selection concept in perfusion/modelfit-related views.
Wed, May 1, 8:15 AM
kompan committed rMITK906ce4ac4140: Repeat corrections for MR Perfusion. (authored by kompan).
Repeat corrections for MR Perfusion.
Wed, May 1, 8:15 AM
kompan committed rMITKa1bd0c09c54e: Remove dead code. (authored by kompan).
Remove dead code.
Wed, May 1, 8:15 AM
kompan committed rMITK8eb45528ac17: Remove OnNodeSelectionChanged and reset mask predicate for PET. (authored by kompan).
Remove OnNodeSelectionChanged and reset mask predicate for PET.
Wed, May 1, 8:15 AM
kompan committed rMITKffaf3da5fac1: Reset mask predicate. (authored by kompan).
Reset mask predicate.
Wed, May 1, 8:15 AM
kompan committed rMITK7acf10d1152a: Use the mitkMultiLabelNodePredicateHelper in curve descriptive parameters view. (authored by kompan).
Use the mitkMultiLabelNodePredicateHelper in curve descriptive parameters view.
Wed, May 1, 8:15 AM
kompan committed rMITK2f14d924c089: Remove OnNodeSelectionChanged. (authored by kompan).
Remove OnNodeSelectionChanged.
Wed, May 1, 8:15 AM
kompan committed rMITK61e77a7bff1a: Remove dead code. (authored by kompan).
Remove dead code.
Wed, May 1, 8:15 AM
kompan committed rMITK4cb395b1b500: Same correction steps for PET as for generic data fitting view. (authored by kompan).
Same correction steps for PET as for generic data fitting view.
Wed, May 1, 8:15 AM
kompan committed rMITKc8336cd00130: Different slots for image and the mask. (authored by kompan).
Different slots for image and the mask.
Wed, May 1, 8:15 AM
kompan committed rMITK5d06aed0f17a: Use GetMultiLabelSegmentationPredicate instead of constructed predicates. (authored by kompan).
Use GetMultiLabelSegmentationPredicate instead of constructed predicates.
Wed, May 1, 8:15 AM
kompan committed rMITK5629a1bd0df4: Rename function to prevent hidden overloaded virtual function error. (authored by kompan).
Rename function to prevent hidden overloaded virtual function error.
Wed, May 1, 8:15 AM
kompan committed rMITK3c59babcb338: Remove duplicate code. (authored by kompan).
Remove duplicate code.
Wed, May 1, 8:15 AM
kompan committed rMITKecc10778abda: Fix T30217 - Change data selection concept for curve description parameters… (authored by kompan).
Fix T30217 - Change data selection concept for curve description parameters…
Wed, May 1, 8:15 AM
kompan committed rMITK294ad53644d0: Change data selection concept in the PET Dynamic View. (authored by kompan).
Change data selection concept in the PET Dynamic View.
Wed, May 1, 8:15 AM
kompan committed rMITK27f21c3f793c: Fix T30217 - change data selection concept in the Generic Data Fitting View. (authored by kompan).
Fix T30217 - change data selection concept in the Generic Data Fitting View.
Wed, May 1, 8:15 AM

Fri, Apr 19

kompan committed rMITK7a59bd54fe89: Fix a collection of UI bugs in Perfusion and ModelFit. (authored by kompan).
Fix a collection of UI bugs in Perfusion and ModelFit.
Fri, Apr 19, 9:16 AM
kompan committed rMITK891ca05736c7: Fix T30341 - Same location for buttons for T1 and T2 conversion (authored by kompan).
Fix T30341 - Same location for buttons for T1 and T2 conversion
Fri, Apr 19, 9:16 AM
kompan committed rMITK4e930ff758a5: T30278 - Disable conversion tab for descriptive Brix. (authored by kompan).
T30278 - Disable conversion tab for descriptive Brix.
Fri, Apr 19, 9:16 AM
kompan committed rMITK14653aa49d03: T30343, T30339 -Add mask info box to GenericDataFitting, MRPerfusion an… (authored by kompan).
T30343, T30339 -Add mask info box to GenericDataFitting, MRPerfusion an…
Fri, Apr 19, 9:16 AM
kompan committed rMITK788416a6f44e: Fix T30276-Remove AIF image selection when "Select AIF from File" is chosen (authored by kompan).
Fix T30276-Remove AIF image selection when "Select AIF from File" is chosen
Fri, Apr 19, 9:16 AM

Feb 28 2024

kompan moved T27739: Inspection positions deletion in ModelFit not updated in data display. from Backlog to Cycle on the MITK (v2024.06) board.
Feb 28 2024, 9:27 AM · MITK (v2024.06), Cleared
kompan closed T27814: Refactor ModelFit Generic Data Fitting view to use new selection concept as Resolved.

This task is closed and will be worked on as part of task https://phabricator.mitk.org/T30217.

Feb 28 2024, 9:26 AM · MITK (v2024.06), Cleared
kompan moved T29638: ModelFit Inspector crahes sometimes on data selection from Backlog to Cycle on the MITK (v2024.06) board.
Feb 28 2024, 9:23 AM · MITK (v2024.06)
kompan closed T27664: Check conversion from signal to concentration for a turboFLASH sequence as Wontfix.
Feb 28 2024, 9:22 AM · MITK (v2024.06), Cleared
kompan moved T30204: Improve visibility between help files for perfusion from Backlog to Cycle on the MITK (v2024.06) board.
Feb 28 2024, 9:21 AM · Request for Discussion, MITK (v2024.06)

Feb 27 2024

kompan closed T30203: Provide checklist for Fit Generator Demo as Wontfix.

The Fit Generator Demo is no part of the currentl releases, therefore no checklist is provided.

Feb 27 2024, 9:35 AM · MITK (v2024.06)

Feb 26 2024

kompan added a project to T30204: Improve visibility between help files for perfusion: Request for Discussion.
Feb 26 2024, 11:43 AM · Request for Discussion, MITK (v2024.06)
kompan closed T30205: Check and update perfusion user manual as Wontfix.

This task is closed as wontfix since the perfusion ModelFit user manual is not provided anymore. All the information available in the user manual is given via the F1-help/ the plugin documentation at https://docs.mitk.org/2023.12/PluginListPage.html.

Feb 26 2024, 11:42 AM · MITK (v2024.06)
kompan closed T28776: Perfusion DataFit View: Inconsistencies in the signal conversion using the turboFLASH sequence as Wontfix.

This task is closed as wontfix since we decided to not support this conversion method anymore (see https://phabricator.mitk.org/T30225).

Feb 26 2024, 11:38 AM · MITK (v2024.06), Checklist
kompan closed T27350: Refactoring of T1 map calculation/selection for perfusion and CEST as Wontfix.

I looked into the issue in more detail and found that the current implementation of the variable flip angle T_1-mapping cannot be easily replaced with a more general T_1-mapping approach. The reason for this is that not just the T_1-map is calculated but also the signal scaling factor S_0 is determined (which is additionally required for the conversion).

Feb 26 2024, 11:33 AM · MITK (v2024.06)
kompan closed T27746: New data selection concept for Fit Generator Demo View as Wontfix.

The Fit Generator Demo View is not part of the MITK release and is not actively supported anymore for now.

Feb 26 2024, 11:13 AM · MITK (v2024.06)

Feb 15 2024

kompan closed T29620: Check if GenericFitMiniApp supports the needed model as Resolved.

This fitting task was applied not to many cases, therefore AVID batch processing was not required and fitting was done in MITK using the formula parser.

Feb 15 2024, 10:24 AM · Missing Info, MITK, Restricted Project, Restricted Project

Dec 11 2023

kompan added a comment to T24795: ModelFit visualization bug?.

In the current ModelFit Inspector version, the current time point is not marked at all. When moving through the time steps in the Image Navigator all data points are displayed at the same color, the current time point is not highlighted in another color. We should discuss if we want this behaviour back and check if there is a bug due to which this functionality is not present anymore.

Dec 11 2023, 10:43 AM · Auto-closed, MITK, Restricted Project

Dec 5 2023

kompan closed T30200: Update checklist for Perfusion DCE MRI Perfusion Datafit as Resolved.
Dec 5 2023, 11:04 AM · MITK (v2024.06)
kompan closed T30202: Provide checklist for ModelFit Generic Data Fitting as Resolved.
Dec 5 2023, 11:04 AM · MITK (v2024.06)
kompan closed T30201: Provide checklist for ModelFit Inspector View as Resolved.
Dec 5 2023, 11:03 AM · MITK (v2024.06)
kompan closed T30206: Parameter naming in mitkPixelBasedParameterFitImageGeneratorTest and mitkROIBasedParameterFitImageGenerator as Resolved.
Dec 5 2023, 10:55 AM · MITK (v2024.06)
kompan closed T28937: [ModelFit] Rethink mitkT2DecayModel as Resolved.
Dec 5 2023, 10:54 AM · MITK (v2024.06)
kompan closed T27654: Refactor concentration curve converter view to use new selection concept as Resolved.
Dec 5 2023, 10:50 AM · MITK (v2024.06), Cleared
kompan closed T27815: Modelfit Generic Data Fitting missing start parameters as Resolved.
Dec 5 2023, 10:46 AM · MITK (v2024.06)
kompan closed T27671: Concentration Curve Converter: Crash due to baseline avergaing as Resolved.
Dec 5 2023, 10:45 AM · MITK (v2024.06), Cleared
kompan closed T27667: Concentration curve converter view- errors in formula for T2-weighted signal conversion as Resolved.
Dec 5 2023, 10:44 AM · MITK (v2024.06), Cleared

Nov 22 2023

kompan added a comment to T29454: Clarify the versions/editions we publish as installer.

Some more name ideas:
MITK Workbench Plus
MITK Workbench - Advanced Edition
MITK Workbench - Extended Edition
MITK Deluxe (ok, too far, I'll better stop now...)

Nov 22 2023, 11:04 AM · MITK (v2024.06), Request for Discussion

Nov 21 2023

kompan closed T27738: Curve Color selection not possible in ModelFit Inspector view settings as Resolved.

This task is closed due to task duplication and will be further taken care of in https://phabricator.mitk.org/T30238.

Nov 21 2023, 11:40 AM · MITK (v2023.12), Cleared

Nov 14 2023

kompan edited the content of 2023 Week 46 (Mid November).
Nov 14 2023, 9:43 AM

Nov 7 2023

kompan committed rMITKd75ec56551b5: Remove turboFLASH conversion from UIs. (authored by kompan).
Remove turboFLASH conversion from UIs.
Nov 7 2023, 1:06 PM
kompan committed rMITKae2bb372f427: Replace signal to concentration conversion image. (authored by kompan).
Replace signal to concentration conversion image.
Nov 7 2023, 1:06 PM
kompan committed rMITK12c868af1d84: Make AIFImageNodeSelector only visible when DedicatedAIFImage box is checked. (authored by kompan).
Make AIFImageNodeSelector only visible when DedicatedAIFImage box is checked.
Nov 7 2023, 1:06 PM
kompan committed rMITK435bd831b730: Rename AIF field from "AIF mask" to "Arterial Input Function (AIF)". (authored by kompan).
Rename AIF field from "AIF mask" to "Arterial Input Function (AIF)".
Nov 7 2023, 1:06 PM
kompan committed rMITK8672bb60a98e: Update doxygen documentation for MRPerfusionView. (authored by kompan).
Update doxygen documentation for MRPerfusionView.
Nov 7 2023, 1:06 PM
kompan committed rMITK947d6046609d: Remove code from Num2CX settings which was forgotten to be removed as part of… (authored by kompan).
Remove code from Num2CX settings which was forgotten to be removed as part of…
Nov 7 2023, 1:06 PM
kompan committed rMITKb3cb7b42e785: Update doxygen documentation for ConcentrationCurveConverterView. (authored by kompan).
Update doxygen documentation for ConcentrationCurveConverterView.
Nov 7 2023, 1:06 PM
kompan committed rMITK992913ec348a: Remove turboFLASH conversion from ConcentrationCurveConverterView. (authored by kompan).
Remove turboFLASH conversion from ConcentrationCurveConverterView.
Nov 7 2023, 1:06 PM
kompan committed rMITK4956a50d5868: Remove turboFLASH conversion from MRPerfusionView. (authored by kompan).
Remove turboFLASH conversion from MRPerfusionView.
Nov 7 2023, 1:06 PM
kompan committed rMITK22b440a035e7: Remove turboFLASH conversion from MRSignal2ConcentrationMiniApp. (authored by kompan).
Remove turboFLASH conversion from MRSignal2ConcentrationMiniApp.
Nov 7 2023, 1:06 PM

Oct 20 2023

kompan committed rMITK6abc240027ea: Rework concentration via VFA calculation. (authored by kompan).
Rework concentration via VFA calculation.
Oct 20 2023, 9:01 AM
kompan committed rMITK0b87fcd6dbb9: Update documentation of concentration converter plugin. (authored by kompan).
Update documentation of concentration converter plugin.
Oct 20 2023, 9:01 AM
kompan committed rMITK8ba706196b03: Update Plugin-Vendor and Plugin-ContactAddress in manifest_headers.cmake. (authored by kompan).
Update Plugin-Vendor and Plugin-ContactAddress in manifest_headers.cmake.
Oct 20 2023, 9:01 AM
kompan committed rMITK4e0a50f5100d: Change initialization order. (authored by kompan).
Change initialization order.
Oct 20 2023, 9:01 AM
kompan committed rMITK7851e8afc722: Update documentation for concentration curve converter view. (authored by kompan).
Update documentation for concentration curve converter view.
Oct 20 2023, 9:01 AM
kompan committed rMITK85de3250c276: Apply the same changes to MRPerfusionView as for… (authored by kompan).
Apply the same changes to MRPerfusionView as for…
Oct 20 2023, 9:01 AM
kompan committed rMITK28999fe8945d: Check before the conversion if the variables were initialized by the user. (authored by kompan).
Check before the conversion if the variables were initialized by the user.
Oct 20 2023, 9:01 AM
kompan committed rMITK0b3d514a1d43: Minor correction regarding decimal number. (authored by kompan).
Minor correction regarding decimal number.
Oct 20 2023, 9:01 AM
kompan committed rMITK4770de677c17: Initialize all variable set by the user to NaN. (authored by kompan).
Initialize all variable set by the user to NaN.
Oct 20 2023, 9:01 AM
kompan committed rMITK0633ae0e4599: Const correctness in mitkConvertToConcentrationViaT1Functor. (authored by kompan).
Const correctness in mitkConvertToConcentrationViaT1Functor.
Oct 20 2023, 9:01 AM
kompan committed rMITKea09b917e043: Use explicit c++ conversions instead of implicit c conversions in… (authored by kompan).
Use explicit c++ conversions instead of implicit c conversions in…
Oct 20 2023, 9:01 AM
kompan committed rMITK7b0f715d9d0d: Initialize m_RepetitionTime in the ConcentrationCurveGenerator constructor. (authored by kompan).
Initialize m_RepetitionTime in the ConcentrationCurveGenerator constructor.
Oct 20 2023, 9:01 AM
kompan committed rMITKb55b2ac41413: Adapt concentration conversion unit test to changes in VFA method. (authored by kompan).
Adapt concentration conversion unit test to changes in VFA method.
Oct 20 2023, 9:01 AM
kompan committed rMITKe46aa60c931e: Minor correction, remove unnecessary MITK_INFO lines. (authored by kompan).
Minor correction, remove unnecessary MITK_INFO lines.
Oct 20 2023, 9:01 AM
kompan committed rMITK3ce3ad1c19e6: Rename Variable Flip Angle Parameters box. (authored by kompan).
Rename Variable Flip Angle Parameters box.
Oct 20 2023, 9:01 AM
kompan committed rMITKaec21bcba0c5: Make baseline averaging available for all conversion methods for 4D images. (authored by kompan).
Make baseline averaging available for all conversion methods for 4D images.
Oct 20 2023, 9:01 AM
kompan committed rMITK0444dd5a1eba: Rework concentration via VFA calculation. (authored by kompan).
Rework concentration via VFA calculation.
Oct 20 2023, 9:01 AM

Oct 18 2023

kompan added a comment to T30227: Link error between plugins F1-Help files.

At the moment it is not very elegant to generate plugin-dependencies just for the documentation. And this solution also does't allow for having references in two-ways between plugins (refer plugin B in plugin A and vice versa). A different approach could be an additional entry in the manifest_header.cmake just for documentation dependecies or to take all references into account for all plugins.

Oct 18 2023, 11:23 AM · MITK
kompan updated the task description for T30227: Link error between plugins F1-Help files.
Oct 18 2023, 11:06 AM · MITK

Oct 17 2023

kompan added a comment to T29454: Clarify the versions/editions we publish as installer.

For the bigger MITK Workbench version of the 2023.10 release it is planned to include Pharmacokinetics (Perfusion, PET) and ModelFit.
Specifically, the following plugins will be included:

Oct 17 2023, 12:40 PM · MITK (v2024.06), Request for Discussion