Draft version #24

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montigno wants to merge 26 commits into master from draft_version

MRIFileManager/DictionaryMRI_System.yml

100644 → 100755

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MRIFileManager/DictionaryMRI_User.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -45,39 +45,39 @@ dictionaryMRI:
  
                       description: {info: ""}

                       whereBruker:  {file: acqp, keyName: $ACQ_grad_matrix=, type: int, format: ~, units: ~}

                       viewer: {category: cineASL}

                       json:   {tagJson: ACQ_grad_matrix, type: string, format: ~, units: ~}  

      ACQ_fov:

                       description: {info: ""}

                       whereBruker:  {file: acqp, keyName: $ACQ_fov=, type: int, format: ~, units: ~}

                       viewer: {category: cineASL}

                       json:   {tagJson: ACQ_fov, type: string, format: ~, units: ~}

      ACQ_slice_sepn:

                       description: {info: ""}

                       whereBruker:  {file: acqp, keyName: $ACQ_slice_sepn=, type: int, format: ~, units: ~}

                       viewer: {category: cineASL}

                       json:   {tagJson: ACQ_slice_sepn, type: string, format: ~, units: ~}

      ACQ_NSLICES:

                       description: {info: ""}

                       whereBruker:  {file: acqp, keyName: $NSLICES=, type: int, format: ~, units: ~}

                       viewer: {category: cineASL}

                       json:   {tagJson: ACQ_NSLICES, type: string, format: ~, units: ~}

      ACQ_slice_thick:

                       description: {info: ""}

                       whereBruker:  {file: acqp, keyName: $ACQ_slice_thick=, type: int, format: ~, units: ~}

                       viewer: {category: cineASL}

                       json:   {tagJson: ACQ_slice_thick, type: string, format: ~, units: ~}

    @@ -153,22 +153,6 @@ dictionaryMRI:
  
                       viewer: {category: cineASL}

                       json:   {tagJson: PVM_SPackArrSliceOrient, type: string, format: ~, units: ~}

      Reception_Gain:

                       description: {info: ""}

                       whereBruker:  {file: acqp, keyName: $RG=, type: int, format: ~, units: ~}

                       viewer: {category: MRI parameters}

                       json:   {tagJson: ~, type: ~, format: ~, units: ~}

      Reception_Gain_Calibrated:

                       description: {info: ""}

                       whereBruker:  {file: acqp, keyName: $ACQ_CalibratedRG=, type: int, format: ~, units: ~}

                       viewer: {category: MRI parameters}

                       json:   {tagJson: ~, type: ~, format: ~, units: ~}

      RECO_offset:

                       description: {info: ""}

    @@ -645,13 +629,6 @@ dictionaryMRI:
  
                      viewer: {category: MRI parameters}

                      json:   {tagJson: MinEchoTime, type: float, format: ~, units: ~}

      RefPower:

                      description: {info: ""}

                      whereBruker:  {file: method, keyName: $PVM_RefPowCh1=, type: string, format: ~, units: ms}

                      viewer: {category: MRI parameters}

                      json:   {tagJson: RefPower, type: string, format: ~, units: ms}

      RefPulse1:

                      description: {info: ""}

                      whereBruker:  {file: method, keyName: $RefPulse1=(, type: string, format: ~, units: ms}

MRIFileManager/MRIManager.jar

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MRIFileManager/MRIManager.sh

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		@@ -1 +1 @@
		java -Xms512m -Xmx4096m -jar MRIManager.jar
		java -Xms512m -Xmx8192m -jar MRIManager.jar

MRIFileManager/MRIManager_lib/JavaEWAH-0.7.9.jar

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MRIFileManager/MRIManager_lib/commons-codec-1.4.jar

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MRIFileManager/MRIManager_lib/commons-logging-1.1.1.jar

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MRIFileManager/MRIManager_lib/flatlaf-3.7.jar

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MRIFileManager/MRIManager_lib/httpclient-4.1.3.jar

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MRIFileManager/MRIManager_lib/httpcore-4.1.4.jar

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MRIFileManager/MRIManager_lib/jsch-0.1.50.jar

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MRIFileManager/MRIManager_lib/org.eclipse.jgit-3.5.0.201409260305-r.jar

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MRIFileManager/Updater.jar

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MRIFileManager/dist/IJ_Prefs.txt

-Original file line number
+Diff line change
@@ -1,102 +1,101 @@
     #ImageJ 1.54f Preferences
-    #Fri Apr 11 08:29:39 CEST 2025
-    .VolumeViewer.alphaMode=0
-    .VolumeViewer.ambientValue=0.5
+    #Tue Mar 19 16:13:03 CET 2024
+    .VolumeViewer.renderMode=0
     .VolumeViewer.backgroundColor=-16763803
-    .VolumeViewer.degreeX=90.0
-    .VolumeViewer.degreeY=-0.0
-    .VolumeViewer.degreeZ=0.0
-    .VolumeViewer.diffuseValue=0.5
-    .VolumeViewer.dist=-98.0
-    .VolumeViewer.interpolationMode=1
-    .VolumeViewer.lightBlue=0
+    fps=7.0
+    new.slices=1
+    .editor.dir=/home/omontigon/Bureau/
+    .VolumeViewer.showTF=true
+    roicolor=\#FFFF00
+    .threshold.raw=false
+    .threshold.loc=789,441
+    .VolumeViewer.zAspect=10.239999771118164
+    div-by-zero=Infinity
+    new.height=400
+    raw.options=2
+    fcolor=\#FFFF00
     .VolumeViewer.lightGreen=128
-    .VolumeViewer.lightRed=255
-    .VolumeViewer.lutNr=0
-    .VolumeViewer.objectLightValue=0.5
-    .VolumeViewer.renderMode=4
-    .VolumeViewer.sampling=0.10000000149011612
-    .VolumeViewer.scale=3.482198476791382
-    .VolumeViewer.shineValue=17.149999618530273
-    .VolumeViewer.showAxes=true
-    .VolumeViewer.showClipLines=false
+    raw.offset=0
     .VolumeViewer.showSlices=false
-    .VolumeViewer.showTF=true
-    .VolumeViewer.specularValue=0.5
+    .VolumeViewer.sampling=1.0
+    .VolumeViewer.lutNr=0
+    .VolumeViewer.scale=1.0
+    .VolumeViewer.interpolationMode=1
+    noise.sd=25.0
+    raw.n=10
+    .VolumeViewer.dist=0.0
+    raw.type=2
+    ij.y=256
+    ij.x=590
+    jpeg=75
+    pp.width=600
+    .log.width=1866
+    raw.height=128
     .VolumeViewer.useLight=false
-    .VolumeViewer.windowHeight=978
-    .VolumeViewer.windowWidthImageRegion=1258
-    .VolumeViewer.windowWidthSlices=327
+    .results.loc=190,636
+    .log.height=1053
+    .VolumeViewer.objectLightValue=0.5
+    .manager.loc=1108,338
+    .log.loc=2076,27
+    showcolor=\#00FFFF
+    prefs.options=4210692
+    measurements=19
+    new.width=400
+    precision=3
     .VolumeViewer.xloc=1920
-    .VolumeViewer.yloc=0
-    .VolumeViewer.zAspect=5.0
-    .b&c.loc=699,455
-    .command-finder.close=false
-    .editor.case-sensitive=true
-    .editor.dir=/home/omontigon/Bureau/
-    .fonts.loc=826,211
+    .VolumeViewer.lightRed=255
+    .VolumeViewer.lightBlue=0
     .gui.scale=1.0
-    .log.height=400
-    .log.loc=852,277
-    .log.width=500
-    .manager.loc=1381,290
+    .VolumeViewer.yloc=0
+    .VolumeViewer.ambientValue=0.5
+    pp.fontsize=14
+    raw.width=128
+    new.fill=0
+    .VolumeViewer.diffuseValue=0.5
+    bcolor=\#FFFFFF
+    menu.size=15
+    dir.image=/home/olivier/Documents/dataIRM/Bruker/VC_stimul/
+    .b&c.loc=1112,341
     .point.size=1
-    .point.type=0
-    .results.height=353
-    .results.loc=447,602
-    .results.width=592
     .threshold.dark=false
-    .threshold.loc=789,441
-    .threshold.mode=1
     .threshold.no-reset=true
-    .threshold.raw=false
-    .toolbar.tool04=Window Level Tool
-    .toolbar.tool05=Command Finder Action Tool
-    ap.options=64
-    bcolor=\#FFFFFF
-    dir.image=/home/olivier/Documents/dataIRM/Nifti/CEST_Rachel_2025/tube_a_b_c_d_e_2/
-    div-by-zero=Infinity
-    fcolor=\#FFFF00
-    fps=7.0
-    ij.x=969
-    ij.y=48
-    jpeg=75
-    measurements=23
-    menu.size=15
-    new.fill=0
-    new.height=400
-    new.slices=1
-    new.type=0
-    new.width=400
-    noise.sd=25.0
-    pp.fontsize=14
+    recent14=/home/omontigon/Documents/dataIRM/Bruker/Mous/Traitements_fevrier2023/20220328-ArgR9-J4/20220328-ArgR9-J4-08-1-T2map_MSME-2022-04-01144636_T2map.nii.gz
+    .VolumeViewer.windowWidthImageRegion=1261
+    recent13=/home/omontigon/Documents/dataIRM/Bruker/Mous/Traitements_fevrier2023/20220328-ArgR2-J4/20220328-ArgR2-J4-16-1-T2map_MSME-2022-04-01115109_T2map.nii.gz
+    recent12=/home/omontigon/Documents/mri_works_atlas/mouse/badhwar/badhwar_hippocampal_atlas_masked.nii
+    recent11=/home/omontigon/Documents/MP3_projects/Raw_data/MRFUSE_20230301-D00-WIP_MRF_Brain_3T_20230309-120519095.nii
+    recent10=/tmp/test_irm/test_irm-05-12_DCE_test_benj_orientation-2016-05-11140044.nii
+    .results.width=598
+    .VolumeViewer.alphaMode=0
+    .point.type=0
+    .threshold.mode=1
     pp.height=340
+    .VolumeViewer.showAxes=true
+    new.type=0
+    recent09=/home/omontigon/Documents/mri_works_atlas/mouse/badhwar/bha_labels_sba.nii
+    recent08=/home/omontigon/dataIRM/CEA-preeclampsie/Registration/souris_F92_PC1/RoiSet_manual.zip
     pp.options=0
-    pp.width=600
-    precision=3
-    prefs.options=4341760
+    recent07=/home/olivier/Documents/dataIRM/Nifti/MicroFlam/Mif-S19-SD6H/Tractography/ADC_map.nii
     prefs.options2=2048
+    recent06=/home/olivier/Documents/dataIRM/Nifti/MicroFlam/Mif-S19-SD6H/Tractography/FA_map.nii
+    recent05=/home/olivier/Documents/dataIRM/Nifti/GluCEST/mapgluCESTj2/APPPS10_99g-04-gluCEST_RARE-2024-01-22113400.nii
+    recent04=/home/olivier/Documents/dataIRM/Nifti/GluCEST/mapgluCESTj2/APPPS10_99g-07-gluCEST_RARE-2024-01-22113400.nii
+    recent03=/home/olivier/Documents/dataIRM/Bruker/Project_Nantes/Nantes_Nude_14_231220_Nantes_Nude_14_231220-09-1-08_T1_RARE_GADOLINIUM_IRMmulti-(E9).nii.gz
+    recent02=/home/olivier/Documents/dataIRM/Bruker/MicroFlam/240126_Mif-S19-SD6H_1_Mif-S19-SD6H-240126_11_1_5_T2map_1SliceME_150um_2av-(E11)-01.nii.gz
+    recent01=/home/olivier/Documents/dataIRM/Bruker/MicroFlam/Mif-S18-SD3H_Mif-S18-SD3H-240126-13-1-7_DTPI_4seg_16dir_sat_150x0.8_b200-600-1200_av2_phLR-(E13).nii.gz
+    .command-finder.close=false
+    recent00=/home/olivier/Documents/dataIRM/Bruker/VC_stimul/Rois_concombre.zip
+    .VolumeViewer.degreeZ=17.0
+    .VolumeViewer.degreeY=41.0
+    .VolumeViewer.degreeX=115.0
+    .VolumeViewer.windowWidthSlices=324
+    ap.options=64
+    .VolumeViewer.specularValue=0.5
+    .VolumeViewer.shineValue=17.149999618530273
+    .VolumeViewer.showClipLines=false
+    .fonts.loc=826,211
+    .VolumeViewer.windowHeight=1017
+    .toolbar.tool05=Command Finder Action Tool
+    .toolbar.tool04=Window Level Tool
     raw.gap=0
-    raw.height=64
-    raw.n=60
-    raw.offset=0
-    raw.options=2
-    raw.type=2
-    raw.width=64
-    recent00=/home/olivier/Documents/dataIRM/Nifti/CEST_Rachel_2025/Tube_a4_b4_c4_d1_d3_2/ROIs_IJ.zip
-    recent01=/home/olivier/Documents/dataIRM/Nifti/CEST/20221004-GdMR9-J17/20221004-GdMR9-J17-05-T1map_RARE.nii
-    recent02=/home/olivier/Documents/dataIRM/Nifti/CEST/Modif_Rachel/Rat8_modif.jpg
-    recent03=/home/olivier/Documents/dataIRM/Nifti/CEST/Modif_Rachel/Rat8_modif.tif
-    recent04=/home/olivier/Documents/dataIRM/Nifti/CEST/Modif_Rachel/Macro_Rat8.ijm
-    recent05=/home/olivier/Documents/dataIRM/Nifti/CEST/Modif_Rachel/Macro_Rat9.ijm
-    recent06=/home/olivier/Documents/dataIRM/Nifti/CEST/20221004-GdMR8-J24/20221004-GdMR8-J24-07-T1map_RARE-T1map.nii
-    recent07=/home/olivier/Documents/dataIRM/Nifti/CEST/20221004-GdMR8-J17/20221004-GdMR8-J17-05-T1map_RARE-T1map.nii
-    recent08=/home/olivier/Documents/dataIRM/Nifti/CEST/20221004-ArgMR8-J10/20221004-ArgMR8-J10-06-T1map_RARE.nii
-    recent09=/tmp/-04-1-1_T2_RARE_80x80x200_85sl-(E4).nii
-    recent10=/tmp/-06-1-MGE-(E6)-02.nii.gz
-    recent11=/tmp/-06-1-MGE-(E6)-01.nii.gz
-    recent12=/home/olivier/Documents/dataIRM/tmp/CEST_new_method/TB55_24/Rois_Ga_Gb1_Gb2.zip
-    recent13=/home/olivier/Documents/dataIRM/Bruker/VC_stimul/Rois_concombre.zip
-    recent14=/home/olivier/Documents/dataIRM/Bruker/MicroFlam/Mif-S18-SD3H_Mif-S18-SD3H-240126-13-1-7_DTPI_4seg_16dir_sat_150x0.8_b200-600-1200_av2_phLR-(E13).nii.gz
-    roicolor=\#FFFF00
-    showcolor=\#00FFFF
+    .results.height=384

MRIFileManager/mri_conv.png

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