Directory mrUtilities/File/Varian/

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justin 2010-06-03 10:59 Rev.: 1693

swaped a line to check for dimensions after dimensions are adjusted to avoid meaningless warning.
Added a header comment to explain how to use outputName argument.

9 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2nifti.m (+9 -5)

justin 2010-03-31 21:09 Rev.: 1677

Check for whether nav echoes have been removed

21 lines of code changed in 3 files:

• mrUtilities/File/Varian: getfidk.c (+21 -14), getfidk.mexmaci (changed), getfidk.mexmaci64 (changed)

justin 2010-03-31 14:13 Rev.: 1676

Calculation for lines of k-space was done inappropriately - it assumed one navigator echo. To accomodate sequences with multiple nav echoes we now check the parameter ni instead of nv

14 lines of code changed in 2 files:

• mrUtilities/File/Varian: getfidk.c (+14 -17), getfidk.mexmaci64 (changed)

justin 2010-03-31 11:55 Rev.: 1675

Fixing code to correctly drop out any reference volumes

27 lines of code changed in 2 files:

• mrUtilities/File/Varian: fid2nifti.m (+8 -1), fid2xform.m (+19 -32)

justin 2010-03-16 15:29 Rev.: 1673

Fix to adjustDims to handle images with more than one volume

6 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2nifti.m (+6 -1)

justin 2010-03-11 21:09 Rev.: 1671

Adding ability to extract only a portion of the image

55 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2nifti.m (+55 -6)

justin 2010-03-10 13:31 Rev.: 1664

oops. shifted pss array in wrong direction

3 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+3 -2)

justin 2010-03-10 11:36 Rev.: 1663

Making a fix for non-integer shifts that were not accounted for in the program fftw3rd. This adjusts the pss array to match the fact that the images were not actually shifted to exactly where they should have been, but were essentially half a voxel off in the slice dimension. The fix is to adjust the pss array to match what is in the image

41 lines of code changed in 2 files:

• mrUtilities/File/Varian: fid2xform.m (+40), getfid.m (+1 -1)

justin 2010-03-03 12:07 Rev.: 1649

Default output arguments

1 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2nifti.m (+1)

justin 2010-02-18 13:32 Rev.: 1641

Making some changes to allow returning one image when multiple receivers were used

42 lines of code changed in 4 files:

• mrUtilities/File/Varian: fid2nifti.m (+27 -11), fid2xform.m (+13 -9), getfid.m (+1), readprocpar.m (+1 -1)

justin 2010-02-03 21:27 Rev.: 1635

change to comments

5 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2nifti.m (+5 -1)

justin 2010-02-03 21:19 Rev.: 1634

Adding ability to shift pro

77 lines of code changed in 4 files:

• mrUtilities/File/Varian: fid2nifti.m (+19 -4), fid2niftihdr.m (+6 -3), fid2xform.m (+17 -7), getfid.m (+35 -11)

justin 2010-02-01 22:24 Rev.: 1632

For files that only have one slice, it doesn't make sense to compute the voxspacing from the difference of the thk (in fact, voxel spacing across slices isn't important). So, you procpar thk for voxspacing in this case.

5 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+5)

justin 2010-01-19 16:11 Rev.: 1627

Check for whether a file has been processed or not added

7 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+7)

justin 2010-01-18 17:27 Rev.: 1626

quietly deal with unprocessed epi files by setting voxel dimensions to nan

13 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+13 -5)

justin 2010-01-18 15:23 Rev.: 1625

Fixing 3d pss slice order. There was a bit of confusion here. Before the code had:

procpar.pss = -procpar.pss
and had the rotation matrix basically undoing this.

But that isn't right. fid2nifti always orders slices from smallest to largest pss, so we don't have to reverse order in fid2xform. In fact, we should just assume that is the case so the offset to the first slice is always the min(pss). Which is what the code now does.

18 lines of code changed in 2 files:

• mrUtilities/File/Varian: fid2nifti.m (+3 -1), fid2xform.m (+15 -10)

justin 2010-01-14 21:35 Rev.: 1623

For 3d scans, there was an erroneously line of code assuming that the 1st and 2nd dimensions were necessarily the same. Removed.

0 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (-1)

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:

• mrUtilities/File/Varian: fid2xform.m (+1 -1)

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

Get time of scan

20 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+20)

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

program to list fid files

26 lines of code changed in 1 file:

• mrUtilities/File/Varian: fiddir.m (new 26)

(35 more)