December 2009 Commit Log

Number of Commits:
67
Number of Active Developers:
2
justin 2009-12-24 20:55 Rev.: 1616

Acceleration factor only applies to phase-encode dimension. It looks like there was some code that was compensating for using ni as readout dimension and not np/2

1 lines of code changed in 1 file:

justin 2009-12-20 21:13 Rev.: 1615

Changing name of function. Also adding ability to get mean roi. Changing calling convention.

521 lines of code changed in 2 files:

justin 2009-12-20 21:12 Rev.: 1614

Adding utility function to cat two cell arrays together

24 lines of code changed in 1 file:

justin 2009-12-20 20:21 Rev.: 1613

Adding to mrUtilities

66 lines of code changed in 1 file:

eli 2009-12-19 04:28 Rev.: 1612

removed a stray ctranspose (') from a callback function (@mlrDisplayEPIdeselectAll) on line 119

3 lines of code changed in 1 file:

justin 2009-12-18 13:58 Rev.: 1611

Ability to display multiple frames and multiple scans at the same time

89 lines of code changed in 1 file:

justin 2009-12-18 13:53 Rev.: 1610

Get time of scan

20 lines of code changed in 1 file:

justin 2009-12-18 13:53 Rev.: 1609

program to list fid files

26 lines of code changed in 1 file:

justin 2009-12-18 13:52 Rev.: 1608

Check to make sure the Raw TSeries don't have . in the name

1 lines of code changed in 1 file:

justin 2009-12-18 13:51 Rev.: 1607

Adding option to drop any filenames that have too many .'s in them. This is really annoying because then you can't get the extension properly from the filename. So it should be prevented right from the start.

19 lines of code changed in 1 file:

eli 2009-12-18 02:39 Rev.: 1606

Added an option to import both right and left hemisphere surfaces. If bothHemiFlag is set to 1, then the function loads the inner and outer surfaces for both hemispheres, concatenates them together, and creates a single baseAnat with both hemispheres. Having both hemispheres loaded up in MLR is convenient for data viewing and it makes extending/restricting ROI's easier when the ROI exists in both hemispheres. Still need to add a hook in MLR GUI to make bothHemiFlag an option.

96 lines of code changed in 1 file:

justin 2009-12-17 22:39 Rev.: 1605

Better checking to see whether there is an existing figure before trying to close

5 lines of code changed in 1 file:

justin 2009-12-17 22:38 Rev.: 1604

fid2niftihdr returns info now too. fid2xform better verbose checking for quiet operation

5 lines of code changed in 2 files:

justin 2009-12-17 22:36 Rev.: 1603

Checkbox to allow viewing of all slices at once

42 lines of code changed in 1 file:

justin 2009-12-17 22:35 Rev.: 1602

Allow for default arguments so that you don't have to have a dialog box come up

17 lines of code changed in 1 file:

justin 2009-12-17 14:49 Rev.: 1601

np is the lenght of the read-out (x2 because it is real+imaginary). ni is the number of phase-encode lines not including navigators.

1 lines of code changed in 1 file:

justin 2009-12-14 16:48 Rev.: 1600

d.data had to be cleared in the code. If you happened to concat a longer scan with a shorter scan, it would crash the code because of a matrix dimension mismatch. This is fixed now.

1 lines of code changed in 1 file:

justin 2009-12-12 09:31 Rev.: 1599

Better help info, also puts all base anatomy overlays into a single overlay that gets stored in the sessions analysis file

24 lines of code changed in 1 file:

justin 2009-12-12 00:13 Rev.: 1598

minor

2 lines of code changed in 1 file:

justin 2009-12-12 00:13 Rev.: 1597

Check for smartfig

3 lines of code changed in 1 file:

justin 2009-12-12 00:12 Rev.: 1596

Making overlayNum/Name more permissive, you can now pass either a name or a number to viewSet for curOVerlay and viewGet for overlayNum

7 lines of code changed in 2 files:

justin 2009-12-11 23:59 Rev.: 1595

Can now save the overlay back into scan dimensions so they can be viewed in MLR

57 lines of code changed in 1 file:

justin 2009-12-11 23:58 Rev.: 1594

help info on how to run

1 lines of code changed in 1 file:

justin 2009-12-11 23:21 Rev.: 1593

Initial version of function that averages overlays across subjects using Caret aligned atlas brains. Right now it just does the averaging, displays the originals and the averaged overlay. Next will work on getting it to add the averaged overlays back to the subjects analyses.

2 lines of code changed in 1 file:

justin 2009-12-11 23:18 Rev.: 1592

Check existence of atlasDir

1 lines of code changed in 1 file:

justin 2009-12-11 23:17 Rev.: 1591

Minor. Better error handeling

11 lines of code changed in 2 files:

justin 2009-12-11 23:16 Rev.: 1590

Import the tSeries by having saveNewTSeries reload the nifti file. This makes sure that scanParams info gets pulled from the nifti file. Otherwise it was losing sform/qform, pixdim info etc.

2 lines of code changed in 1 file:

justin 2009-12-11 17:53 Rev.: 1589

pass back the actual original overlay values in another field (before it just passed back RGB values )

9 lines of code changed in 1 file:

justin 2009-12-11 17:52 Rev.: 1588

Minor change so that if a base is not loaded you can still call refreshMLRDisplay from a script without an error

9 lines of code changed in 1 file:

justin 2009-12-11 17:52 Rev.: 1587

error dialogs changed to mrErrorDlg

4 lines of code changed in 1 file:

justin 2009-12-11 16:20 Rev.: 1586

More intelligent warning when your framePeriod is set wrong, and you get a very long length for you hdrlen

4 lines of code changed in 1 file:

justin 2009-12-11 16:18 Rev.: 1585

accept 2 input arguments

1 lines of code changed in 1 file:

justin 2009-12-11 16:17 Rev.: 1584

TR computation has to correct for acc factor

6 lines of code changed in 1 file:

justin 2009-12-11 16:13 Rev.: 1583

Save mrSession after relinking stimfiles

2 lines of code changed in 1 file:

justin 2009-12-11 16:06 Rev.: 1582

Overlay name can be substituted for overlayNum

4 lines of code changed in 1 file:

justin 2009-12-11 16:05 Rev.: 1581

Checks input arguments and is more flexible about names - i.e. adds default nifti extension if ommitted. Analysis name can omit directory name if same as analysis name

15 lines of code changed in 2 files:

justin 2009-12-11 11:32 Rev.: 1580

more informative help message

1 lines of code changed in 1 file:

justin 2009-12-11 11:32 Rev.: 1579

Test on d structure to prevent crashing if missing analysis

2 lines of code changed in 1 file:

justin 2009-12-11 11:30 Rev.: 1578

adding dry-run

24 lines of code changed in 1 file:

justin 2009-12-11 11:29 Rev.: 1577

preallocate space for ROIs. Speeds up loading quite a bit....

3 lines of code changed in 1 file:

justin 2009-12-11 11:27 Rev.: 1576

minor: print help info instead of crashing when you call with no arguments

9 lines of code changed in 2 files:

justin 2009-12-10 17:14 Rev.: 1575

Adding a "resampled destination" menu item to File. This works like "resampled source" except it resamples the destination volume to create an inplane from the canonical volume. The resolution of the resulting images has the same inplane dimensions as the volume (usualy 1x1) with the same slice thickness as the inplanes. This should be useful if you don't collect inplane anatomies but instead collect an alignment volume. Then you would load your 3D volume as the destination and the epis as your source and then run this function to generate a high resolution anatomy.

67 lines of code changed in 2 files:

justin 2009-12-10 15:03 Rev.: 1574

For 2D images with multiple receivers. Varian swaps the order of the slice and receiver dimensions... This commits fix that.

40 lines of code changed in 6 files:

justin 2009-12-10 13:48 Rev.: 1573

Fixing number of navechoes for flash images (should be 0)

18 lines of code changed in 5 files:

justin 2009-12-09 20:51 Rev.: 1572

adding verbose print out when swapping slices

1 lines of code changed in 1 file:

justin 2009-12-09 17:29 Rev.: 1571

Cleaning up code a little bit -- making all procpar reading happen in fid2xform rather than in both places

33 lines of code changed in 2 files:

justin 2009-12-09 16:20 Rev.: 1570

readprocpar checks for correct extension

1 lines of code changed in 1 file:

justin 2009-12-09 16:20 Rev.: 1569

fix2xform and fid2nifti now handles interleaved slices correctly

18 lines of code changed in 3 files:

justin 2009-12-09 15:41 Rev.: 1568

set extension. changing the way the voxel skip size is computed to be median instead of mean.

4 lines of code changed in 2 files:

justin 2009-12-09 15:20 Rev.: 1567

split out fid2niftihdr function, updated readprocpar to read the number navigator echoes correctly, and recompiled getfidk.c which has some changes in message reporting

112 lines of code changed in 6 files:

justin 2009-12-09 14:09 Rev.: 1566

Minor fix

2 lines of code changed in 3 files:

justin 2009-12-09 14:02 Rev.: 1565

Updating getfidk so that it reads the number of navigator echoes correctly. Should be the field "navecho" in the procpar x the number of shots divided by the acceleration factor (which are found from the petable name.

35 lines of code changed in 3 files:

justin 2009-12-08 16:28 Rev.: 1564

Removed function calls to old handlers from mrInterrogator (no need to retain old hooks, I think). Plus the code was giving warnings in matlab79

3 lines of code changed in 1 file:

justin 2009-12-03 23:34 Rev.: 1563

comments

2 lines of code changed in 1 file:

justin 2009-12-03 23:31 Rev.: 1562

Changed to write curvature files to atlas directory and then load them from there on subsequent calls to save processing time

41 lines of code changed in 1 file:

justin 2009-12-03 23:10 Rev.: 1561

Better searching/reading of atlas display surfaces. Adding getArgs. Negating curvature so that fundus is back and gyrus is white.

102 lines of code changed in 1 file:

justin 2009-12-03 21:45 Rev.: 1560

Working import

133 lines of code changed in 2 files:

justin 2009-12-03 21:45 Rev.: 1559

Call with path to surface

10 lines of code changed in 1 file:

justin 2009-12-03 21:44 Rev.: 1558

Check for proper command line arguments

4 lines of code changed in 1 file:

justin 2009-12-03 21:44 Rev.: 1557

Changed cortical depth slider so arrows jump by 0.1, clicking inside slider steps by 0.5 instead of vice versa which was non-intuitive

2 lines of code changed in 2 files:

justin 2009-12-03 19:49 Rev.: 1556

First pass at importing surfaces from a Caret alignment done with script mypreborder.sh and mypostborder.sh. Not fully functional yet.

691 lines of code changed in 4 files:

justin 2009-12-03 19:47 Rev.: 1555

Used to have volume crop dimensions hard coded to 176x256x256. Now you have the option to adjust this

26 lines of code changed in 2 files:

justin 2009-12-03 19:47 Rev.: 1554

function to read xform from freesurfer text file

64 lines of code changed in 1 file:

justin 2009-12-03 19:45 Rev.: 1553

error message for when epirri has not been run

6 lines of code changed in 2 files:

justin 2009-12-02 22:07 Rev.: 1552

added function to load xforms from text file

56 lines of code changed in 1 file:

justin 2009-12-02 21:20 Rev.: 1551

Making a Caret directory

527 lines of code changed in 4 files:

justin 2009-12-01 06:47 Rev.: 1550

Fixing a bug that Taosheng found

13 lines of code changed in 2 files:

November 2009 »

Generated by StatSVN 0.4.1