Directory mrUtilities/File/Varian/

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justin 2012-01-17 21:05 Rev.: 2425

fid2nifti reads nifti extension from mrPref

2 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2nifti.m (+2 -2)

justin 2011-12-15 10:35 Rev.: 2402

Slice order for data linked to a FID

8 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+8)

justin 2011-10-26 22:57 Rev.: 2365

Adding ability to keep reference volumes

3 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2nifti.m (+3 -3)

justin 2011-10-19 12:19 Rev.: 2363

Adding ability to select which receiver you want to load or inf for all receivers - for Varian/Agilant fid files

11 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2nifti.m (+11 -4)

justin 2011-10-19 11:38 Rev.: 2361

adding 32 bit binary file

0 lines of code changed in 1 file:

• mrUtilities/File/Varian: getfidkraw.mexmaci (new)

justin 2011-10-04 12:12 Rev.: 2359

processed 3D files no longer need to have x-axis flipped (this only applies to pre-console upgrade data)

2 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+2 -9)

justin 2011-10-04 10:27 Rev.: 2358

mlrVol now clips the brightest / darkest points in an image (by default set to the top/bottom 0.2% of pixels, but can be adjusted in the GUI). This helps for display of images that have a stray bright pixel. The readout value when you mouse over points will still display the unclipped value.

getfidk gives a better warning for old files that did not have epi processing run

fid2xform has a few fixes for old data. For one, the epi is not flipped relative to the 2D/3D images, so we don't need to do that. Also, the X dimension is reversed in the old data, so needed to compensate for that

13 lines of code changed in 2 files:

• mrUtilities/File/Varian: fid2xform.m (+12 -6), getfidk.m (+1)

justin 2011-09-30 15:41 Rev.: 2346

Minor fixes to deal with bad fid files

14 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+14)

justin 2011-09-30 15:17 Rev.: 2345

Fixing xform for 8 channel data which apparently is flipped in the x dimension relative to the 4 channel data. Minor fixes here and there to mlrVol and mlrImageXform

14 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+14 -10)

justin 2011-09-29 10:23 Rev.: 2341

Fixing problem loading new 2D anatomy images - apparently the receivers and volumes are no longer swapped

7 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+7 -2)

justin 2011-09-29 09:35 Rev.: 2338

Fixing the middle of the pss - needs to be shifted but (not) in the header

3 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+3 -4)

justin 2011-09-12 16:24 Rev.: 2322

fid2nifti now by default scales output values to between 0 and 255. This should not change the resolution of the data but allows it to pass happily through freesurfer which seems to think that values under 1 should be thresholded to 0

13 lines of code changed in 2 files:

• mrUtilities/File/Varian: fid2nifti.m (+12 -3), fid2niftihdr.m (+1 -1)

justin 2011-09-12 16:05 Rev.: 2321

Fix to xform for epi images, the offset was being calculated incorrectly

7 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2xform.m (+7 -3)

justin 2011-09-07 17:19 Rev.: 2308

tweaking xforms.
fid2xform works better for old volumes by not applying voxel shift
fdf2xform works on many of the 3D volumes (but not double oblique) offsets are slightly incorrect still and does not work well at all on the 2D anatomy files

43 lines of code changed in 3 files:

• mrUtilities/File/Varian: fdf2nifti.m (+32 -40), fid2xform.m (+10 -8), getfid.m (+1 -1)

justin 2011-09-07 15:01 Rev.: 2307

Fixing up fid2nifti code so that it correctly handles shifting the center of the pss dimension for 3D volumes.

Also, you can now pass movepss through the arguments and it will movepss and generate a correct xform

fdf2nifti has a *more* correct (but still broken) xform

70 lines of code changed in 5 files:

• mrUtilities/File/Varian: fdf2nifti.m (+39 -10), fid2nifti.m (+7 -5), fid2niftihdr.m (+3 -3), fid2xform.m (+16 -5), getfid.m (+5 -2)

justin 2011-09-06 22:09 Rev.: 2303

changeset allows passing of arguments from functions that use mlrImageParseArgs to the load routines. For example you can set movepro or kspace and that will get passed to fid2nifti.

Also implements grabbing a portion of the image by setting xMin, xMax, yMin, yMax, zMin and zMax -> these will return that portion of the image and make sure the xform is still correct

14 lines of code changed in 2 files:

• mrUtilities/File/Varian: fid2nifti.m (+7 -4), fid2niftihdr.m (+7 -3)

justin 2011-09-06 16:07 Rev.: 2301

Adding ability to movepro and movepss for 3D images

48 lines of code changed in 1 file:

• mrUtilities/File/Varian: getfid.m (+48 -24)

justin 2011-09-06 13:48 Rev.: 2300

Fixing reading and writing of complex edt files (real/complex) should be interleaved in data file

42 lines of code changed in 5 files:

• mrUtilities/File/Varian: fid2xform.m (+3 -4), getfid.m (+4), getfidk.m (+5), readsdt.m (+29 -55), writesdt.m (+1 -1)

justin 2011-09-06 12:12 Rev.: 2299

Check for fft23dexe processing - which means we do a 2D rather than 3D fourier transform on data - and also needs
to have the X axis flipped

17 lines of code changed in 2 files:

• mrUtilities/File/Varian: fid2xform.m (+16 -3), getfid.m (+1 -1)

justin 2011-09-05 16:53 Rev.: 2292

This changeset implements writing out data in sdt/spr edt/epr format

3 lines of code changed in 1 file:

• mrUtilities/File/Varian: fid2nifti.m (+3 -3)

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