July 2007 Commit Log

Number of Commits:
74
Number of Active Developers:
6
david 2007-07-31 00:12 Rev.: 452

Modified Files:
mrAlignGUI.m refreshAlignDisplay.m

Deal with NaNs when loading volumes and setting clip range.

25 lines of code changed in 3 files:

frakkopesto 2007-07-28 00:50 Rev.: 451

Fixed motion compensation loading file (NAN mean).

2 lines of code changed in 1 file:

farshadm 2007-07-27 05:42 Rev.: 450

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30 lines of code changed in 1 file:

david 2007-07-25 07:45 Rev.: 449

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1 lines of code changed in 1 file:

david 2007-07-25 07:41 Rev.: 448

Modified Files:
motionComp.m motionCompWithinScan.m sliceTimeCorrect.m

Added slice time correction without motion compensation

36 lines of code changed in 3 files:

david 2007-07-25 07:20 Rev.: 447

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246 lines of code changed in 5 files:

david 2007-07-24 04:47 Rev.: 446

Modified Files:
motionComp.m motionCompReconcileParams.m motionCompWithinScan.m

Added slice time correction

171 lines of code changed in 8 files:

david 2007-07-24 04:46 Rev.: 445

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3 lines of code changed in 1 file:

justin 2007-07-23 07:56 Rev.: 444

rendering parameters for flats. multiple load of flats. removed warning about transforms not being implemented.

68 lines of code changed in 2 files:

justin 2007-07-22 07:43 Rev.: 443

minor fixes to get rois working for flat maps

30 lines of code changed in 1 file:

justin 2007-07-22 07:38 Rev.: 442

setup to read more than one flat map at a time

86 lines of code changed in 1 file:

justin 2007-07-22 07:36 Rev.: 441

for flat anatomies, there is now a field called baseCoordMap which contains fields for the underlying volume dimensions and coordinate maps. viewGet returns this structure or empty if it doesn't exist

11 lines of code changed in 2 files:

justin 2007-07-22 04:06 Rev.: 440

smoothing and thresholding flat map

21 lines of code changed in 1 file:

justin 2007-07-22 04:05 Rev.: 439

added rconv2

50 lines of code changed in 1 file:

justin 2007-07-21 07:39 Rev.: 438

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16 lines of code changed in 1 file:

justin 2007-07-21 07:39 Rev.: 437

changes to deal with flat coordinates

49 lines of code changed in 3 files:

farshadm 2007-07-21 05:20 Rev.: 436

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3 lines of code changed in 1 file:

farshadm 2007-07-21 04:55 Rev.: 435

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38 lines of code changed in 1 file:

farshadm 2007-07-21 03:31

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38 lines of code changed in 6 files:

eli 2007-07-21 02:19 Rev.: 432

calls nanmean instead of mean (useful when ROI contains NaNs from motion comp runs)

2 lines of code changed in 1 file:

eli 2007-07-21 01:33 Rev.: 431

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6 lines of code changed in 1 file:

justin 2007-07-20 23:10 Rev.: 430

started function to loadFlat

121 lines of code changed in 2 files:

justin 2007-07-20 23:10 Rev.: 429

added menu item for load flat

13 lines of code changed in 1 file:

justin 2007-07-20 22:53 Rev.: 428

added load flat menu item

0 lines of code changed in 1 file:

eli 2007-07-20 11:07 Rev.: 427

added afni stimfile type

88 lines of code changed in 1 file:

david 2007-07-20 07:57 Rev.: 426

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0 lines of code changed in 2 files:

david 2007-07-20 07:44 Rev.: 425

Modified Files:
mrLoadRetGUI.fig mrLoadRetGUI.m

Added Edit > ROI > Info dialog

23 lines of code changed in 2 files:

david 2007-07-20 07:25 Rev.: 424

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19 lines of code changed in 1 file:

david 2007-07-20 07:05 Rev.: 423

Modified Files:
mrAlignGUI.fig mrAlignGUI.m

Added "Compute EPI Alignment"

6 lines of code changed in 2 files:

david 2007-07-20 06:57 Rev.: 422

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73 lines of code changed in 1 file:

david 2007-07-20 06:21 Rev.: 421

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5 lines of code changed in 1 file:

david 2007-07-20 06:14 Rev.: 420

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15 lines of code changed in 4 files:

justin 2007-07-20 03:55 Rev.: 419

fixed numbers line 0.123e-7 to convert properly

1 lines of code changed in 1 file:

justin 2007-07-20 01:11 Rev.: 418

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3 lines of code changed in 1 file:

david 2007-07-20 00:10 Rev.: 417

Modified Files:
computeAlignment.m intensityContrastCorrection.m mrAlignGUI.m

Added capability that will be useful for aligning EPIs.
Modified Files:
motionComp.m motionCompBetweenScans.m motionCompWithinScan.m

Added capability for slice time correction.
Modified Files:
clip.m estMotion3.m estMotionInterp3.m estMotionIter3.m
estMotionMulti3.m warpAffine3.m warpAffineInterp3.m

Added capability for complex valued images and for phase-images. This will be useful for aligning EPIs.

204 lines of code changed in 7 files:

david 2007-07-20 00:09 Rev.: 416

Modified Files:
computeAlignment.m intensityContrastCorrection.m mrAlignGUI.m

Added capability that will be useful for aligning EPIs.
Modified Files:
motionComp.m motionCompBetweenScans.m motionCompWithinScan.m

Added capability for slice time correction.

5 lines of code changed in 4 files:

david 2007-07-20 00:09 Rev.: 415

Modified Files:
computeAlignment.m intensityContrastCorrection.m mrAlignGUI.m

Added capability that will be useful for aligning EPIs.

15 lines of code changed in 3 files:

farshadm 2007-07-19 21:42 Rev.: 414

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2 lines of code changed in 2 files:

justin 2007-07-19 04:28 Rev.: 413

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2 lines of code changed in 1 file:

justin 2007-07-18 06:57 Rev.: 412

mrStr2num so that str2num doesn't inadvertently call the str as a function

47 lines of code changed in 4 files:

justin 2007-07-18 06:57 Rev.: 411

remove importROIdir preference at startup

2 lines of code changed in 1 file:

justin 2007-07-18 06:56 Rev.: 410

minor change

1 lines of code changed in 1 file:

david 2007-07-18 06:51 Rev.: 409

Modified Files:
viewGet.m

Added sliceOrder
Simplified nslices, slicedims, datasize, and tseriesSize

45 lines of code changed in 1 file:

david 2007-07-18 06:51 Rev.: 408

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221 lines of code changed in 2 files:

farshadm 2007-07-18 06:25 Rev.: 407

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28 lines of code changed in 4 files:

eli 2007-07-18 06:19 Rev.: 406

eliminated more redundant code...

41 lines of code changed in 1 file:

david 2007-07-18 05:53 Rev.: 405

Modified Files:
motionCompGUI.fig motionCompGUI.m motionCompReconcileParams.m

Added slice time correction checkbox to motionCompGUI

148 lines of code changed in 3 files:

david 2007-07-18 03:28 Rev.: 404

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132 lines of code changed in 4 files:

david 2007-07-18 03:10 Rev.: 403

Modified Files:
mrLoadRetGUI.fig mrLoadRetGUI.m

Cleaned up callback function names and reordered.

150 lines of code changed in 2 files:

david 2007-07-18 02:48 Rev.: 402

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231 lines of code changed in 1 file:

david 2007-07-18 02:47 Rev.: 401

Modified Files:
corAnal.m corAnalMergeParams.m

Eliminated code in corAnal that was redundant with corAnalMergeParams

3 lines of code changed in 3 files:

david 2007-07-18 01:12 Rev.: 400

Added Files:
estMotionInterp3.m warpAffineInterp3.m

These functions enable slice time correction simultaneously with motion compensation,
using 4d interpolation in space and time.

233 lines of code changed in 2 files:

farshadm 2007-07-18 00:38 Rev.: 399

eventtimes stimfiles now can specify stimdurations_s (duration of stimulus/event
in seconds). the duration is zero corresponds to a single frame in the design matrix.
otherwise if stimulus spans multiple TRs then the multiple rows in the design matrix
will be set to one

glm analysis can use TR supersampling to more accurately model the hemodynamic changes
evoked by stimuli that are not synchronous with the TR or have variable durations.

62 lines of code changed in 5 files:

farshadm 2007-07-17 06:56 Rev.: 398

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1 lines of code changed in 1 file:

shani 2007-07-17 00:46 Rev.: 397

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1 lines of code changed in 1 file:

farshadm 2007-07-17 00:29 Rev.: 396

checks if callback field exists (does not fail if callback is not set)

9 lines of code changed in 1 file:

justin 2007-07-17 00:26 Rev.: 395

baseVolumes loading properly

7 lines of code changed in 1 file:

justin 2007-07-17 00:26 Rev.: 394

importROI remembers directory

6 lines of code changed in 1 file:

justin 2007-07-17 00:25 Rev.: 393

compute roi coordinates usine linear coordinates in intersect (speeds up things by a factor of 3 over using intersect with rows)

37 lines of code changed in 1 file:

justin 2007-07-17 00:25 Rev.: 392

deal with headers that don't have an sform

1 lines of code changed in 1 file:

justin 2007-07-13 07:14 Rev.: 391

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1 lines of code changed in 1 file:

justin 2007-07-13 07:09 Rev.: 390

save mrSession after setting mrSetPref since it kept losing the preference in mrEditPrefs because mrGetPref reloads from disk

1 lines of code changed in 1 file:

justin 2007-07-13 06:38 Rev.: 389

gParams.callback needed to be init

30 lines of code changed in 2 files:

justin 2007-07-12 01:53 Rev.: 388

callback parameters for buttons

12 lines of code changed in 1 file:

farshadm 2007-07-11 00:54 Rev.: 387

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1 lines of code changed in 1 file:

eli 2007-07-07 08:02 Rev.: 386

added mrGetPref call to get niftiFileExtension

7 lines of code changed in 1 file:

david 2007-07-07 07:42 Rev.: 385

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0 lines of code changed in 1 file:

david 2007-07-07 07:41 Rev.: 384

Modified Files: refreshMLRDisplay.m

Fixed bug with ROI drawing. When first running mrLoadRet, it used to open a separate figure because of the 'hold on' line.
Replaced this by specifying 'Parent' in each call to 'line':

line([y(i)-w,y(i)+w,y(i)+w,y(i)-w,y(i)-w],...
[x(i)-w,x(i)-w,x(i)+w,x(i)+w,x(i)-w], ...
'Color',color,'LineWidth',lineWidth,'Parent',gui.axis);

197 lines of code changed in 1 file:

david 2007-07-07 07:38 Rev.: 383

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1 lines of code changed in 1 file:

david 2007-07-07 02:59 Rev.: 382

mrLoadRet.m
added close to close the extra window that comes up
this is a temporary fix for a bug that for some unknown reason opens the extra figure

Modified Files:
isanalysis.m isbase.m isgroup.m isoverlay.m isroi.m isscan.m isview.m mrOpenWindow.m viewSet.m

Changed these functions so that they can return either 1 or 2 values. If only 1 value returned, then it is logical true or false.
If 2 values are returned, then it is of the form:

[check analysis] = isanalysis(analysis)

that tries to fix the structure while checking it. In particular, each structure has some optional fields that get filled with default values.

Changed calls to these functions in various places (mostly mrLoadRetGUI and viewSet) to make use of defaults.

1520 lines of code changed in 9 files:

david 2007-07-07 02:56 Rev.: 381

mrLoadRet.m
added close to close the extra window that comes up
this is a temporary fix for a bug that for some unknown reason opens the extra figure

106 lines of code changed in 7 files:

eli 2007-07-06 23:48 Rev.: 380

created separate loop for warpAffine3 in full motion comp. also cleared 'tseriesIC' before this new loop. these changes were necessary b/c i was running out of memory running motion comp on large high-res datasets.

40 lines of code changed in 1 file:

eli 2007-07-06 08:55 Rev.: 379

added call to loadMrDefaults

5 lines of code changed in 1 file:

justin 2007-07-02 21:55 Rev.: 378

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52 lines of code changed in 1 file:

June 2007 »

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