April 2008 Commit Log

Number of Commits:

71

Number of Active Developers:

4

eli 2008-04-30 01:15 #71 Rev.: 1078

Made a modification to makeFlat.m that will get the orientation of the flat patch correct, most of the time. Will no longer need flipFlag, but keep it for now, just in case.

1 lines of code changed in 1 file:

• mrLoadRet/File: loadFlatOFF.m (+1 -1)

eli 2008-04-30 01:14 #70 Rev.: 1077

Large modification: Now check the winding direction (i.e., CW vs. CCW) of the faces on the flat patch and the 3D surfaces. If there is a mismatch in direction between the two, do an X-Y swap of the vertices in the flat patch. This seems to get the orientation correct on the patches that I've tested.

71 lines of code changed in 1 file:

• mrLoadRet/Analysis: makeFlat.m (+71 -11)

justin 2008-04-29 07:08 #69 Rev.: 1076

base structure saved out with saveAlignment had data in it!

3 lines of code changed in 1 file:

• mrAlign: mrAlignGUI.m (+3)

farshadm 2008-04-29 03:56 #68 Rev.: 1075

GLM can do processing on chunks of data smaller than one slice. "all" is
accepted as the contrast for eventRelatedGlmGUI.

73 lines of code changed in 3 files:

• mrLoadRet/Analysis/EventRelated: eventRelatedGlm.m (+68 -25), eventRelatedGlmGUI.m (+1 -1), getGlmContrast.m (+4 -4)

eli 2008-04-29 03:00 #67 Rev.: 1074

*** empty log message ***

2 lines of code changed in 1 file:

• mrLoadRet/File: loadFlatOFF.m (+2 -2)

eli 2008-04-29 00:46 #66 Rev.: 1073

fixed small type

1 lines of code changed in 1 file:

• mrLoadRet/File: loadFlatOFF.m (+1)

eli 2008-04-29 00:20 #65 Rev.: 1072

Added a parameter to allow flipping flat patches. This is necessary for some patches that come out X-Y revered for some mysterious reason.

12 lines of code changed in 1 file:

• mrLoadRet/File: loadFlatOFF.m (+12 -3)

eli 2008-04-26 07:17 #64 Rev.: 1071

now 'right' is really right and 'rostral' is rostral in patch coloring

1 lines of code changed in 1 file:

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

justin 2008-04-26 04:59 #63 Rev.: 1070

show what warping based on scan2scan transform does.

104 lines of code changed in 1 file:

• mrLoadRet/Plot: mrEpiMovie.m (+104 -28)

justin 2008-04-26 04:58 #62 Rev.: 1069

handle string fields

13 lines of code changed in 1 file:

• mrUtilities/MatlabUtilities: mrParamsSet.m (+13 -1)

shani 2008-04-26 04:43 #61 Rev.: 1068

added a check for isbase to be safer when grab vol2mag and vol2tal

2 lines of code changed in 1 file:

• mrLoadRet/Analysis: makeFlat.m (+2)

shani 2008-04-26 04:22 #60 Rev.: 1067

Added vol2mag and vol2tal

13 lines of code changed in 1 file:

• mrLoadRet/Analysis: makeFlat.m (+13)

shani 2008-04-26 04:13 #59 Rev.: 1066

Added viewGet for baseCoordMapPath, and made mrFlatMesh the default

4 lines of code changed in 1 file:

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

justin 2008-04-23 01:44 #58 Rev.: 1065

for dealing with memory overflow: runs event-related analysis on a subset of rows at a time

114 lines of code changed in 4 files:

• mrLoadRet/Analysis/EventRelated: eventRelated.m (+40 -23), getNumSlicesAtATime.m (+35 -8), getr2.m (+3 -3), loadScan.m (+36 -15)

justin 2008-04-23 01:43 #57 Rev.: 1064

prints more stuff when called from command line

10 lines of code changed in 1 file:

• mrLoadRet/File: scanInfo.m (+10 -3)

justin 2008-04-23 01:43 #56 Rev.: 1063

viewGet scanQform

11 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (+11)

justin 2008-04-21 21:00 #55 Rev.: 1062

minor change to error message

1 lines of code changed in 1 file:

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

justin 2008-04-21 21:00 #54 Rev.: 1061

minor changes. allowing group name to be passed in instead of group num for some parameters.

52 lines of code changed in 2 files:

• mrLoadRet/View: viewGet.m (+35 -10), viewSet.m (+17 -6)

justin 2008-04-21 20:58 #53 Rev.: 1060

Add force argument

14 lines of code changed in 1 file:

• mrLoadRet/File: mrCleanDir.m (+14 -6)

justin 2008-04-17 21:31 #52 Rev.: 1059

check for empty overlay

5 lines of code changed in 1 file:

• mrLoadRet/File: overlayInfo.m (+5)

justin 2008-04-17 21:30 #51 Rev.: 1058

save originating path

1 lines of code changed in 1 file:

• mrLoadRet/File: loadSurface.m (+1)

justin 2008-04-17 21:29 #50 Rev.: 1057

plot/surfaceViewer just like plot/flatViewer

9 lines of code changed in 1 file:

• mrLoadRet/GUI: mrLoadRetGUI.m (+9 -3)

justin 2008-04-17 21:28 #49 Rev.: 1056

Show surface viewer menu item when a surface is loaded

3 lines of code changed in 1 file:

• mrLoadRet/GUI: mlrGuiSet.m (+3 -1)

justin 2008-04-17 21:28 #48 Rev.: 1055

minor fix for when calling with the names of all fiels

4 lines of code changed in 1 file:

• mrLoadRet/GUI: mrSurfViewer.m (+4 -3)

justin 2008-04-17 21:27 #47 Rev.: 1054

always close the flat viewer when done

3 lines of code changed in 1 file:

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

justin 2008-04-17 21:26 #46 Rev.: 1053

more robust clipping values when displaying image

16 lines of code changed in 1 file:

• mrLoadRet/Plot: mrEpiMovie.m (+16 -2)

justin 2008-04-17 21:25 #45 Rev.: 1052

changes to allow for path variable in surfaces as well as flats

8 lines of code changed in 2 files:

• mrLoadRet/View: viewGet.m (+2 -1), viewSet.m (+6 -1)

eli 2008-04-15 07:19 #44 Rev.: 1051

really got rid of the extra plots of the flattened output

7 lines of code changed in 1 file:

• mrUtilities/surfUtils: flattenSurfaceMFM.m (+7 -3)

justin 2008-04-15 07:15 #43 Rev.: 1050

changed the direction of the x axis to make the surfaces render in the correct orientation

6 lines of code changed in 1 file:

• mrLoadRet/GUI: refreshMLRDisplay.m (+6 -8)

eli 2008-04-15 04:44 #42 Rev.: 1049

got rid of annoying plots of flat mesh

2 lines of code changed in 1 file:

• mrUtilities/surfUtils: flattenSurfaceMFM.m (+2 -2)

justin 2008-04-12 04:07 #41 Rev.: 1048

Small fix so that both Volume and Gray ROIs can be imported

1 lines of code changed in 1 file:

• mrLoadRet/ROI: importROI.m (+1 -1)

justin 2008-04-12 04:06 #40 Rev.: 1047

small display glitch that caused x-axis to sometimes show-up reversed. Essentially the axis directions need to be set by hand rather than the default which is that matlab autosets them

11 lines of code changed in 2 files:

• mrLoadRet/GUI: mrFlatViewer.m (+6), mrSurfViewer.m (+5 -4)

eli 2008-04-12 00:49 #39 Rev.: 1046

used to add 2 to the vertices in writePatchOFF. deleted this because it isn't necessary.

1 lines of code changed in 1 file:

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

justin 2008-04-11 23:35 #38 Rev.: 1045

print out of how much coordinates have been shifted by

3 lines of code changed in 1 file:

• mrUtilities/File/Nifti: xformSurfaceWorld2Array.m (+3)

justin 2008-04-11 23:35 #37 Rev.: 1044

added filename to structure

1 lines of code changed in 1 file:

• mrLoadRet/File: loadSurfOFF.m (+1)

justin 2008-04-11 12:08 #36 Rev.: 1043

didn't need another +1 offset for C to matlab since jonas' xform from mlrXformFromHeader handles that

0 lines of code changed in 1 file:

• mrUtilities/File/Nifti: xformSurfaceWorld2Array.m (-2)

justin 2008-04-11 05:15 #35 Rev.: 1042

viewSet for a baseCoordMap

8 lines of code changed in 1 file:

• mrLoadRet/View: viewSet.m (+8)

justin 2008-04-11 05:14 #34 Rev.: 1041

minor comment change

1 lines of code changed in 1 file:

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

justin 2008-04-11 05:14 #33 Rev.: 1040

Added ability to edit surface names and path

34 lines of code changed in 1 file:

• mrLoadRet/Edit: editBaseGUI.m (+34 -1)

eli 2008-04-11 02:03 #32 Rev.: 1039

*** empty log message ***

7 lines of code changed in 1 file:

• mrLoadRet/File: reshapeTSeries.m (+7 -6)

eli 2008-04-11 01:50 #31 Rev.: 1038

fixed small typo (coords1) in setxor call

1 lines of code changed in 1 file:

• mrLoadRet/ROI: combineROIs.m (+1 -1)

eli 2008-04-11 01:41 #30 Rev.: 1037

got rid of X-Y swapping

18 lines of code changed in 2 files:

• mrLoadRet/Analysis: calcDist.m (+5), makeFlat.m (+13 -12)

eli 2008-04-11 01:39 #29 Rev.: 1036

got rid of the X-Y swapping

6 lines of code changed in 1 file:

• mrLoadRet/File: loadFlatOFF.m (+6 -6)

justin 2008-04-11 00:55 #28 Rev.: 1035

implemented changes needed to handle the world2array xform that jonas' surfrelax tools assume. Basically the analyze header had fields pixdim(6:8) which is an offset and that needs to shift the origin of the coordinates in the surfaces to get them into array coordinates. This is now handled by a function xformSurfaceWorld2Array which also handles the necessary 0 to 1 based coordinate frame change. We also removed all x/y swaps which were unnecessary. loadSurfOFF was swapping xy and then we later swapped them back in loadSurface and loadFlatOFF.

80 lines of code changed in 7 files:

• mrLoadRet/File: loadFlatOFF.m (+3), loadSurfOFF.m (-17), loadSurface.m (+10 -4), writeOFF.m (+6 -3)
• mrLoadRet/GUI: mrFlatViewer.m (+24 -14), mrSurfViewer.m (+31 -5)
• mrUtilities/File/Nifti: xformSurfaceWorld2Array.m (+6 -1)

justin 2008-04-11 00:12 #27 Rev.: 1034

function from jonas which does world2array xform for surfaces. Note that there is a minor change that allows passing in a header instead of a filename

93 lines of code changed in 1 file:

• mrUtilities/File/Nifti: mlrXFormFromHeader.m (new 93)

eli 2008-04-11 00:09 #26 Rev.: 1033

added 'basehdr' -- returns the nifti header of the current base anatomy

9 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (+9)

justin 2008-04-11 00:01 #25 Rev.: 1032

*** empty log message ***

42 lines of code changed in 1 file:

• mrUtilities/File/Nifti: xformSurfaceWorld2Array.m (new 42)

eli 2008-04-10 07:06 #24 Rev.: 1031

changed a mrErrorDlg to a mrWarnDlg

2 lines of code changed in 1 file:

• mrLoadRet/View: viewSet.m (+2 -2)

eli 2008-04-10 06:56 #23 Rev.: 1030

intel recompile after justin fixed edge handling

0 lines of code changed in 1 file:

• mrUtilities/ImageProcessing: myCinterp3.mexmaci (changed)

justin 2008-04-10 06:18 #22 Rev.: 1029

fixed problem dereferencing outside the volume

10 lines of code changed in 2 files:

• mrUtilities/ImageProcessing: myCinterp3.c (+10 -1), myCinterp3.mexmac (changed)

justin 2008-04-10 04:59 #21 Rev.: 1028

check for empty concatInfo

3 lines of code changed in 1 file:

• mrLoadRet/Analysis/EventRelated: getStimvol.m (+3 -3)

justin 2008-04-10 04:59 #20 Rev.: 1027

delete view at end

1 lines of code changed in 1 file:

• mrLoadRet/File: mrCleanDir.m (+1)

justin 2008-04-10 04:58 #19 Rev.: 1026

Don't save an empty prefs file

5 lines of code changed in 1 file:

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

justin 2008-04-10 03:41 #18 Rev.: 1025

adding back with -kb flag

0 lines of code changed in 2 files:

• mrAlign: checkAlignmentGUI.fig (new), mrAlignGUI.fig (new)

justin 2008-04-10 03:40 #17 Rev.: 1024

fixing missing -kb flag

0 lines of code changed in 2 files:

• mrAlign: checkAlignmentGUI.fig (changed), mrAlignGUI.fig (changed)

eli 2008-04-10 01:08 #16 Rev.: 1023

*** empty log message ***

2 lines of code changed in 1 file:

• mrLoadRet/File: loadSurfOFF.m (+2 -1)

eli 2008-04-10 00:49 #15 Rev.: 1022

figured out the off by 2 problem. It turns out that Jonas' code was shifting the origin by - the values in pixdim(6:8), which is usually [1 1 1] since that is the voxel size. This issue is still not completely resolved since here we are assuming an offset of [1 1 1], but in some old headers, that was set to [-1 -1 -1] instead.

15 lines of code changed in 1 file:

• mrLoadRet/File: loadSurfOFF.m (+15 -4)

justin 2008-04-09 22:48 #14 Rev.: 1021

if user passes in a string for the roi name first check to see if it is in the view already before reloading

13 lines of code changed in 1 file:

• mrLoadRet/ROI: getROICoordinates.m (+13 -6)

justin 2008-04-09 22:47 #13 Rev.: 1020

warn if user is trying to set a new group to have the same name as an existing group

5 lines of code changed in 1 file:

• mrLoadRet/View: viewSet.m (+5)

justin 2008-04-09 07:15 #12 Rev.: 1019

added kb flag

0 lines of code changed in 3 files:

• mrUtilities/ImageProcessing: corrDn.dll (new), myCinterp3.dll (new), upConv.dll (new)

justin 2008-04-09 07:15 #11 Rev.: 1018

fixing -kb flag

0 lines of code changed in 3 files:

• mrUtilities/ImageProcessing: corrDn.dll (changed), myCinterp3.dll (changed), upConv.dll (changed)

justin 2008-04-09 07:14 #10 Rev.: 1017

adding back files with -kb flag

0 lines of code changed in 12 files:

• mrUtilities/ImageProcessing: corrDn.mexglx (new), corrDn.mexlx (new), corrDn.mexmac (new), corrDn.mexmaci (new), myCinterp3.mexglx (new), myCinterp3.mexlx (new), myCinterp3.mexmac (new), myCinterp3.mexmaci (new), upConv.mexglx (new), upConv.mexlx (new), upConv.mexmac (new), upConv.mexmaci (new)

justin 2008-04-09 07:13 #9 Rev.: 1016

fixing missing -kb flag and removing old mex versions

0 lines of code changed in 22 files:

• mrUtilities/ImageProcessing: corrDn.mex4 (del), corrDn.mexglx (changed), corrDn.mexhp7 (del), corrDn.mexlx (changed), corrDn.mexmac (changed), corrDn.mexmaci (changed), corrDn.mexsol (del), myCinterp3.mex4 (del), myCinterp3.mexa (del), myCinterp3.mexglx (changed), myCinterp3.mexhp7 (del), myCinterp3.mexlx (changed), myCinterp3.mexmac (changed), myCinterp3.mexmaci (changed), myCinterp3.mexsol (del), upConv.mex4 (del), upConv.mexglx (changed), upConv.mexhp7 (del), upConv.mexlx (changed), upConv.mexmac (changed), upConv.mexmaci (changed), upConv.mexsol (del)

eli 2008-04-09 00:23 #8 Rev.: 1015

check for empty roi structures

88 lines of code changed in 1 file:

• mrLoadRet/GUI: mrPrint.m (+88 -86)

justin 2008-04-08 21:50 #7 Rev.: 1014

checks for valid fig handle before getting fig data (this happens when you use viewGet on a view that does not have an open figure)

37 lines of code changed in 1 file:

• mrLoadRet/View: viewGet.m (+37 -13)

justin 2008-04-08 21:49 #6 Rev.: 1013

will add a fourth row of 1's if the roi does not have that

6 lines of code changed in 1 file:

• mrLoadRet/View: isroi.m (+6)

eli 2008-04-08 05:06 #5 Rev.: 1012

removed line that replaced NaN's with 0's.

1 lines of code changed in 1 file:

• mrLoadRet/Analysis/ConcatTSeries: concatTSeries.m (+1 -2)

eli 2008-04-08 04:28 #4 Rev.: 1011

seems to work fine in 7.6 after a week of testing...

1 lines of code changed in 1 file:

• mrLoadRet: mrLoadRetVersion.m (+1 -1)

justin 2008-04-07 22:52 #3 Rev.: 1010

add ability to change interrogator

5 lines of code changed in 1 file:

• mrLoadRet/Edit: editOverlayGUImrParams.m (+5 -1)

justin 2008-04-07 22:51 #2 Rev.: 1009

When changing sforms for base anatomies and scans, it now also changes the pixel dimensions to match what is implied by the sform

24 lines of code changed in 1 file:

• mrLoadRet/View: viewSet.m (+24 -1)

justin 2008-04-07 22:49 #1 Rev.: 1008

If you rename the analysis it now changes the name filed in the structure as well

3 lines of code changed in 1 file:

• mrLoadRet/File: saveAnalysis.m (+3 -1)

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