February 2008 Commit Log

Number of Commits:

69

Number of Active Developers:

5

justin 2008-02-27 02:08 #69 Rev.: 975

Always display warning on command line as well even if set to verbose

4 lines of code changed in 1 file:

• mrUtilities/MatlabUtilities: mrWarnDlg.m (+4 -4)

justin 2008-02-27 02:06 #68 Rev.: 974

Brought out this function from viewGet

34 lines of code changed in 1 file:

• mrUtilities/MatlabUtilities: oneTimeWarning.m (new 34)

justin 2008-02-27 02:06 #67 Rev.: 973

moved oneTimeWarning to mrUtilities

0 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (-14)

justin 2008-02-27 02:01 #66 Rev.: 972

deleteView

5 lines of code changed in 1 file:

• mrLoadRet/File: scanInfo.m (+5)

justin 2008-02-27 02:01 #65 Rev.: 971

check for starting a new view in a different session directory

6 lines of code changed in 1 file:

• mrLoadRet/View: newView.m (+6)

justin 2008-02-25 14:08 #64 Rev.: 970

Switch to doing eventRelated analysis with single precision if there is not enough memory for doing double precision with a single slice at a time.

58 lines of code changed in 6 files:

• mrLoadRet/Analysis/EventRelated: eventRelated.m (+9 -2), getNumSlicesAtATime.m (+24 -4), loadScan.m (+8 -5)
• mrLoadRet/File: loadTSeries.m (+6 -3)
• mrLoadRet/Plot: timecoursePlot.m (+1 -2)
• mrUtilities/File/Nifti: cbiReadNifti.m (+10 -2)

eli 2008-02-22 05:00 #63 Rev.: 969

removed shortcut key for line ROI

0 lines of code changed in 1 file:

• mrLoadRet/GUI: mrLoadRetGUI.fig (changed)

justin 2008-02-22 00:52 #62 Rev.: 968

suppressed qfac==0 warning, according to the nifti documentation this shouldn't happen, but specifies that it is correct to set the qfac=1 for this case. The warning crops up often--perhaps from Analyze files converted to Nifti. But, since this is defined behavior in the standard it seems better just to do it. The warning has only served to confuse people and has never indicated anything wrong with the qforms....

11 lines of code changed in 1 file:

• mrUtilities/File/Nifti: cbiQuaternionToHomogeneous.m (+11 -1)

justin 2008-02-22 00:31 #61 Rev.: 967

chanded error call to mrErrorDlg

52 lines of code changed in 2 files:

• mrUtilities/File/Nifti: cbiWriteNifti.m (+13 -13), cbiWriteNiftiHeader.m (+39 -39)

justin 2008-02-21 13:59 #60 Rev.: 966

errors for when fopen fails

4 lines of code changed in 2 files:

• mrUtilities/File/Nifti: cbiWriteNifti.m (+1), cbiWriteNiftiHeader.m (+3 -1)

justin 2008-02-21 09:03 #59 Rev.: 965

Minor change: newView does not need to have parameter 'Volume', so all calls were changed to be v = newView

32 lines of code changed in 27 files:

• mrAlign: intensityContrastCorrection.m (+1 -1)
• mrLoadRet/Analysis/AverageTSeries: averageTSeries.m (+1 -1)
• mrLoadRet/Analysis/ConcatTSeries: concatTSeriesReconcileParams.m (+1 -1)
• mrLoadRet/Analysis/CorAnal: corAnal.m (+1 -1)
• mrLoadRet/Analysis/EventRelated: eventRelatedGUI.m (+1 -1), eventRelatedGlmGUI.m (+1 -1), eventRelatedReconcileParams.m (+1 -1)
• mrLoadRet/Analysis/MotionComp: dispmotioncorrect.m (+1 -1), motionComp.m (+1 -1), motionCompBetweenScans.m (+1 -1), motionCompGUI.m (+1 -1), motionCompGUImrParams.m (+1 -1), motionCompWithinScan.m (+1 -1), sliceTimeCorrect.m (+1 -1)
• mrLoadRet/Analysis/QuickAnalysis: mrDispOverlay.m (+1 -1)
• mrLoadRet/File: dicomInfo.m (+1 -1), groupInfo.m (+1 -1), importGroupScans.m (+2 -2), loadROITSeries.m (+3 -3), mrCleanDir.m (+2 -2), saveSform.m (+2 -2), scanInfo.m (+1 -1)
• mrLoadRet/GUI: mrParamsDialogSelectScans.m (+1 -1)
• mrLoadRet/View: newView.m (+1 -1)
• mrUtilities/File/Nifti: mrFixNiftiHdr.m (+1 -1), mrSetNiftiTransforms.m (+1 -1), mrUpdateNiftiHdr.m (+1 -1)

justin 2008-02-21 08:55 #58 Rev.: 964

changed number of rows before parmasDialog splits into two columns

4 lines of code changed in 1 file:

• mrUtilities/MatlabUtilities: mrParamsDialog.m (+4 -4)

justin 2008-02-21 08:54 #57 Rev.: 963

Larger interrogator name field

1 lines of code changed in 1 file:

• mrLoadRet/GUI: mrInterrogator.m (+1 -1)

justin 2008-02-21 08:53 #56 Rev.: 962

use stripext instead of strtok

3 lines of code changed in 1 file:

• mrLoadRet/GUI: mrFlatViewer.m (+3 -3)

justin 2008-02-21 08:52 #55 Rev.: 961

small parameter check

5 lines of code changed in 1 file:

• mrLoadRet/GUI: mrPrint.m (+5)

justin 2008-02-21 08:52 #54 Rev.: 960

gets scanQform and scanSform from viewGet

8 lines of code changed in 1 file:

• mrLoadRet/File: scanInfo.m (+8 -5)

justin 2008-02-21 08:51 #53 Rev.: 959

added line of code for keeping overlays as single precision (but it is commented out now, since I don't think it makes much difference).
Added viewGet for scanQform

16 lines of code changed in 2 files:

• mrLoadRet/View: viewGet.m (+10), viewSet.m (+6 -1)

justin 2008-02-21 02:20 #52 Rev.: 958

change to comments

2 lines of code changed in 1 file:

• mrLoadRet/Analysis/ConcatTSeries: concatTSeries.m (+2 -4)

justin 2008-02-21 02:20 #51 Rev.: 957

handles grouped parameters correctly

18 lines of code changed in 1 file:

• mrUtilities/MatlabUtilities: mrParamsDefault.m (+18)

justin 2008-02-21 02:19 #50 Rev.: 956

options to get params by passing in justGetParams=1 and defaultParams=1

40 lines of code changed in 2 files:

• mrLoadRet/Analysis/MotionComp: motionComp.m (+19 -2), motionCompGUImrParams.m (+21 -2)

farshadm 2008-02-20 04:12 #49 Rev.: 955

*** empty log message ***

4 lines of code changed in 1 file:

• mrLoadRet/ROI: getROICoordinates.m (+4 -3)

farshadm 2008-02-20 03:29 #48 Rev.: 954

no change (improve code readability)

5 lines of code changed in 1 file:

• mrLoadRet/File: loadSurfOFF.m (+5 -5)

farshadm 2008-02-20 03:23 #47 Rev.: 953

option for applying highpass filter to the design matrix

28 lines of code changed in 3 files:

• mrLoadRet/Analysis/EventRelated: eventRelated.m (+8 -2), eventRelatedGUI.m (+3 -2), makescm.m (+17 -2)

justin 2008-02-19 23:13 #46 Rev.: 952

fixes variable names that are invalid with fixBadChars

6 lines of code changed in 1 file:

• mrUtilities/MatlabUtilities: mrParamsParse.m (+6)

justin 2008-02-19 23:13 #45 Rev.: 951

changed roi viewGet so that it handles sform_code === 0 by just returning the xform, rather than returning the identity

9 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (+9)

justin 2008-02-19 23:12 #44 Rev.: 950

If sform_code is set to 0 (i.e. no alignment) than roi takes xform from bases qform

12 lines of code changed in 1 file:

• mrLoadRet/ROI: newROI.m (+12 -5)

justin 2008-02-19 23:12 #43 Rev.: 949

groupInfo now has a gui

1 lines of code changed in 1 file:

• mrLoadRet/GUI: mrLoadRetGUI.m (+1 -1)

justin 2008-02-19 23:12 #42 Rev.: 948

added an mrParamsDialog for when this is called from GUI

9 lines of code changed in 1 file:

• mrLoadRet/File: groupInfo.m (+9 -2)

shani 2008-02-19 05:01 #41 Rev.: 947

Making sure that the .mat files being loaded are the correct ones, becuase might have an unrelated .mat file that's not a base structure

13 lines of code changed in 1 file:

• mrAlign: mrAlignGUI.m (+13 -4)

shani 2008-02-19 03:18 #40 Rev.: 946

Made it check for sform_code = 0 or sform_code = []

2 lines of code changed in 1 file:

• mrUtilities/File/Nifti: cbiCreateNiftiHeader.m (+2 -2)

shani 2008-02-19 03:17 #39 Rev.: 945

Made it check for sform_code = 0 or sform_code = []

1 lines of code changed in 1 file:

• mrUtilities/File/Nifti: cbiSetNiftiSform.m (+1 -1)

shani 2008-02-19 03:12 #38 Rev.: 944

Changed so only resets sform_code if it hadn't already been set. Otherwise, don't assume it's =1.

6 lines of code changed in 1 file:

• mrUtilities/File/Nifti: cbiSetNiftiSform.m (+6 -1)

shani 2008-02-19 03:11 #37 Rev.: 943

Changed it so it only sets sform_code to 1 if it was previously not set. Otherwise, just keep sform_code the same as it is in the input.

6 lines of code changed in 1 file:

• mrUtilities/File/Nifti: cbiCreateNiftiHeader.m (+6 -2)

shani 2008-02-15 06:53 #36 Rev.: 942

Made default params.warpBaseScan be the first of the scans being concatenated

11 lines of code changed in 1 file:

• mrLoadRet/Analysis/ConcatTSeries: concatTSeries.m (+11 -7)

justin 2008-02-15 06:44 #35 Rev.: 941

Increased width of drop-down listboxes in GUI
fixed file name parsing bug that confused M for WM (used stripext instead of strtok)

4 lines of code changed in 2 files:

• mrLoadRet/GUI: mrLoadRetGUI.fig (changed), mrSurfViewer.m (+4 -4)

shani 2008-02-15 04:16 #34 Rev.: 940

Fixed the error messages to have the correct function name so it's not confusing when debugging

2 lines of code changed in 1 file:

• mrLoadRet/GUI: mrSurfViewer.m (+2 -2)

shani 2008-02-13 03:57 #33 Rev.: 939

Updated it to set sform_code as well (optional input) and also to set
vol2tal and vol2mag (also optional input)

29 lines of code changed in 1 file:

• mrLoadRet/File: saveSform.m (+29 -4)

shani 2008-02-13 03:55 #32 Rev.: 938

Updated it to save the vol2mag and vol2tal fields

108 lines of code changed in 1 file:

• mrAlign: mrAlignGUI.m (+108 -5)

hallum 2008-02-13 01:40 #31 Rev.: 937

Changed regexp() call to regexpi() (case insensitive) when looking for curvature file.

1 lines of code changed in 1 file:

• mrLoadRet/Analysis: makeFlat.m (+1 -1)

justin 2008-02-12 09:40 #30 Rev.: 936

minor typo fixes

2 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (+2 -1)

justin 2008-02-12 09:38 #29 Rev.: 935

fix textbox heights for intel

5 lines of code changed in 1 file:

• mrUtilities/MatlabUtilities: mrParamsDialog.m (+5 -1)

eli 2008-02-09 01:47 #28 Rev.: 934

*** empty log message ***

1 lines of code changed in 1 file:

• mrLoadRet/Analysis: makeFlat.m (+1 -1)

eli 2008-02-09 01:43 #27 Rev.: 933

needed for dijkstra

0 lines of code changed in 2 files:

• mrUtilities/surfUtils: conio.h (new), fibheap.h (new)

eli 2008-02-09 01:37 #26 Rev.: 932

changed to 'dijkstra2.cpp'

25 lines of code changed in 1 file:

• mrUtilities/surfUtils: dijkstra.cpp (+25 -10)

eli 2008-02-09 01:32 #25 Rev.: 931

*** empty log message ***

5 lines of code changed in 1 file:

• mrLoadRet/Analysis: makeFlat.m (+5 -4)

eli 2008-02-09 01:16 #24 Rev.: 930

changed name of mrFlatMesh calling function to flattenSurfaceMFM

12 lines of code changed in 1 file:

• mrLoadRet/Analysis: makeFlat.m (+12 -17)

eli 2008-02-09 01:15 #23 Rev.: 929

initial import

446 lines of code changed in 1 file:

• mrUtilities/surfUtils: flattenSurfaceMFM.m (new 446)

eli 2008-02-09 01:13 #22 Rev.: 928

initial import of mrFlatMesh surface utilities

10 lines of code changed in 31 files:

• mrUtilities/surfUtils: assignPerimeterPositions.m (new), assignToNearest.c (new), assignToNearest.m (new), assignToNearest.mexmac (new), assignToNearest.mexmaci (new), assignToNearestNew.m (new), connectionBasedSmooth.m (new), correctBadNodes.m (new), dijkstra.cpp (new 10), dijkstra.m (new), dijkstra.mexmac (new), dijkstra.mexmaci (new), find3DNeighbourDists.m (new), findBadPerimNodes.m (new), findConnectionMatrix.m (new), findEdgesInGroup.m (new), findFaceArea.m (new), findFacesInGroup.m (new), findGroupPerimeter.m (new), findLegalPerimeters.m (new), findNPConnection.m (new), findUniqueFaceIndexList.m (new), floodFillFindPerim.m (new), makeMeshImage.m (new), mfmAreaErrorMap.m (new), mfmBuildSubMesh.m (new), orderMeshPerimeterPointsAll.m (new), removeHangingNodes.m (new), scaleConnectionMatrixToDist.m (new), shift.m (new), statusStringAdd.m (new)

justin 2008-02-09 00:11 #21 Rev.: 927

Fixed tilt textbox callback

3 lines of code changed in 1 file:

• mrLoadRet/GUI: mrLoadRetGUI.m (+3 -1)

shani 2008-02-08 06:14 #20 Rev.: 926

Fixed to read in the vol2mag and vol2tal fields from the underlying base anatomy

19 lines of code changed in 1 file:

• mrLoadRet/File: loadSurface.m (+19)

justin 2008-02-08 05:18 #19 Rev.: 925

viewSets were added for scan2base and base2scan

25 lines of code changed in 2 files:

• mrLoadRet/View: viewGet.m (+3 -3), viewSet.m (+22)

justin 2008-02-08 05:17 #18 Rev.: 924

Converted all of these functions to use base2roi,scan2roi etc. This also removed any need to use shiftOriginXform. xformROIcoords was changed to take the xform with the shiftOriginXform composited (instead of compositing within the function) and all calling functions were modified to follow that convention. modifyROI now takes the xform from the coordinates passed in to the rois coordinates, i.e. base2roi instead of putting those things together within the function. Again all calling functions were modified to reflect this change

169 lines of code changed in 9 files:

• mrLoadRet/ROI: combineROIs.m (+7 -5), convertROI.m (+1 -23), convertROICorticalDepth.m (+5 -27), drawROI.m (+2 -2), getROICoordinates.m (+31 -42), modifyROI.m (+3 -5), restrictROI.m (+29 -32), roiInfo.m (+74), xformROIcoords.m (+17 -17)

justin 2008-02-08 05:15 #17 Rev.: 923

Uses base2roi viewGet

22 lines of code changed in 3 files:

• mrLoadRet/GUI: mrFlatViewer.m (+2 -3), mrLoadRetGUI.m (+17 -98), refreshMLRDisplay.m (+3 -4)

justin 2008-02-08 05:15 #16 Rev.: 922

changed names to sform from xform and uses scan2base viewGet

14 lines of code changed in 3 files:

• mrLoadRet/File: baseInfo.m (+1 -1), groupInfo.m (+4 -4), mrExport2SR.m (+9 -14)

justin 2008-02-08 05:14 #15 Rev.: 921

use sacn2roi viewGet

3 lines of code changed in 1 file:

• mrLoadRet/Analysis/SignalProc: tseriesROI.m (+3 -4)

justin 2008-02-08 05:14 #14 Rev.: 920

Changed name of xform to Sform

1 lines of code changed in 1 file:

• mrLoadRet/Analysis/EventRelated: loadScan.m (+1 -1)

justin 2008-02-08 05:14 #13 Rev.: 919

Removed unnecessary xform calls

4 lines of code changed in 4 files:

• mrLoadRet/Analysis: calcDist.m (+1 -5), makeFlat.m (-2)
• mrLoadRet/Analysis/AverageTSeries: averageTSeries.m (+1 -2)
• mrLoadRet/Analysis/ConcatTSeries: concatTSeries.m (+2 -2)

shani 2008-02-08 03:37 #12 Rev.: 918

*** empty log message ***

14 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (+14 -10)

shani 2008-02-08 03:19 #11 Rev.: 917

Added roi2roi, also fixed bug in roi2mag and in scan2scan

209 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (+209 -54)

justin 2008-02-07 13:34 #10 Rev.: 916

used new scan2roi xforms

5 lines of code changed in 1 file:

• mrLoadRet/Analysis: searchForVoxel.m (+5 -8)

shani 2008-02-07 05:25 #9 Rev.: 915

Added scan2roi

115 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (+115 -18)

justin 2008-02-07 02:26 #8 Rev.: 914

does not do warping if the transform is identity

16 lines of code changed in 1 file:

• mrLoadRet/Analysis/ConcatTSeries: concatTSeries.m (+16 -14)

shani 2008-02-07 02:20 #7 Rev.: 913

*** empty log message ***

14 lines of code changed in 2 files:

• mrLoadRet/Analysis/AverageTSeries: averageTSeries.m (+1 -6)
• mrLoadRet/View: viewGet.m (+13 -3)

justin 2008-02-07 01:49 #6 Rev.: 912

Fixed type that did not return the vol2tal properly

2 lines of code changed in 1 file:

• mrLoadRet/File: scanInfo.m (+2 -2)

justin 2008-02-07 01:49 #5 Rev.: 911

Uses scan2scan to do warping. Also passes along vol2mag and vol2tal.

60 lines of code changed in 2 files:

• mrLoadRet/Analysis/AverageTSeries: averageTSeries.m (+21 -7)
• mrLoadRet/Analysis/ConcatTSeries: concatTSeries.m (+39 -9)

justin 2008-02-07 01:48 #4 Rev.: 910

allows passage of a groupName in place of a groupNum for all viewGets that use getScanAndGroup

4 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (+4 -1)

shani 2008-02-06 01:12 #3 Rev.: 909

Added field talPoints to save the points used for the talairach definition, so that if you want to change them you can start at the original points. Usually this field will be empty.

3 lines of code changed in 1 file:

• mrLoadRet/View: isbase.m (+3 -2)

eli 2008-02-05 04:11 #2 Rev.: 908

can now 'Find file' for both inner and outer surfaces

3 lines of code changed in 1 file:

• mrLoadRet/GUI: mrSurfViewer.m (+3)

eli 2008-02-05 02:47 #1 Rev.: 907

fixed removing junk frames before plotting

5 lines of code changed in 1 file:

• mrLoadRet/Plot: timecoursePlot.m (+5 -4)

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