September 2011 Commit Log

Number of Commits:
68
Number of Active Developers:
1
justin 2011-09-30 22:22 Rev.: 2349

Fixes non-updating overlays when displayInterpolated is not set

4 lines of code changed in 1 file:

justin 2011-09-30 22:06 Rev.: 2348

Fixed overlay not always redrawing properly.
Also, after image xform the current display coordinate now gets xformed too so that the image stays in the same place

15 lines of code changed in 2 files:

justin 2011-09-30 17:20 Rev.: 2347

Adding ability to clear xforms

14 lines of code changed in 1 file:

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

Minor fixes to deal with bad fid files

24 lines of code changed in 3 files:

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

18 lines of code changed in 3 files:

justin 2011-09-30 14:09 Rev.: 2344

Adding ability to edit mlrImage headers using an mrParamsDialog - this can be accessed via mlrVol

156 lines of code changed in 3 files:

justin 2011-09-29 21:15 Rev.: 2343

Fixing pixdim xform to be correct for mlrImageXform. Also, can do xform of pixdim even if qform does not exist.
Identity xform for mlrVOl takes voxel size into account

25 lines of code changed in 2 files:

justin 2011-09-29 17:20 Rev.: 2342

Adding ability to save alignment of volumes out and function to display headers.

68 lines of code changed in 2 files:

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

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

8 lines of code changed in 2 files:

justin 2011-09-29 10:08 Rev.: 2340

mlrVol can now do cropping using mlrImageXform. Also fixed some minor issues like checking bounds on the display coordinate which caused crashes if the image dimensions had changed.

23 lines of code changed in 2 files:

justin 2011-09-29 09:36 Rev.: 2339

Adding save control and controls for mlrImageXfrom from mlrVol

178 lines of code changed in 1 file:

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:

justin 2011-09-29 06:35 Rev.: 2337

Moves cropping functionality into mlrImageXform. Also fixes sform as well as qform if it is set

64 lines of code changed in 2 files:

justin 2011-09-23 03:33 Rev.: 2334

Minor change to help info

3 lines of code changed in 1 file:

justin 2011-09-23 00:04 Rev.: 2333

Minor fixes here and there

17 lines of code changed in 2 files:

justin 2011-09-17 17:55 Rev.: 2325

A few fairly minor fixes. mlrImageParseArgs had lost the passing of the orient variable along, fixed that. mlrImageXform now fixes the image dimensions. mlrVol now sets mouse handlers after volumes are brought up so as to avoid errors if the user moved the mouse over the image before everything was set correctly

34 lines of code changed in 3 files:

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

14 lines of code changed in 3 files:

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:

justin 2011-09-12 16:05 Rev.: 2320

Minor change to default parameters

2 lines of code changed in 1 file:

justin 2011-09-11 15:09 Rev.: 2319

changeset allows passing of mlrImageXform arguments through mlrImageParseArgs -> that is, if you do mlrVol or mlrImageLoad you can use arguments like rotateXY or flipX, etc.

34 lines of code changed in 5 files:

justin 2011-09-11 15:08 Rev.: 2318

Helper function to display seconds as a string

35 lines of code changed in 1 file:

justin 2011-09-10 22:13 Rev.: 2317

Adding function that can be used to xform images (and/or) headers. Implements swaping and flipping dimensions, shifting and rotating

218 lines of code changed in 2 files:

justin 2011-09-07 23:39 Rev.: 2310

Adding ability to set resFactor and shifting start position

26 lines of code changed in 1 file:

justin 2011-09-07 23:03 Rev.: 2309

Adding mlrImageReslice - this function reslices a canonical volume with the dimesnions of the epi or other slice passed in as the second argument. That is, you can take your epi images and then generate an inplane anatomy image from your canonical (assuming you have aligned). Note that I still need to work on the exact starting point of the image and allowing passing in arguments for what resolution you want. For now it defaults to doubling the resolution in all dimensions (resFactor = 2)

120 lines of code changed in 2 files:

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:

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

71 lines of code changed in 6 files:

justin 2011-09-07 11:41 Rev.: 2306

Adding ability to load particular volumes of a multivolume image to mlrImageLoad

44 lines of code changed in 2 files:

justin 2011-09-07 10:57 Rev.: 2305

Adding an mlrSmartfig function based on mrGet/SetFigloc functions and fixing all calls to smartfig

84 lines of code changed in 8 files:

justin 2011-09-06 22:09 Rev.: 2304

minor comment change

2 lines of code changed in 1 file:

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

152 lines of code changed in 6 files:

justin 2011-09-06 16:07 Rev.: 2302

Small check for when data strucutre rather than data matrix is passed in

10 lines of code changed in 1 file:

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:

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:

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:

justin 2011-09-06 11:17 Rev.: 2298

Fixing mlrImageGetAxisLabels to return a structure rather than lots of separate arrays

talairach now tests for LPI image orientation and gives warning if not in correct orientation

53 lines of code changed in 5 files:

justin 2011-09-06 10:54 Rev.: 2297

mlrImageOrient can now orient to any valid orietation like LPI or RAS
ALso, better check for empty image

27 lines of code changed in 4 files:

justin 2011-09-05 23:04 Rev.: 2296

Fixes bug in xform needed to use forward rather than reverse axis mapping

1 lines of code changed in 1 file:

justin 2011-09-05 22:40 Rev.: 2295

Adding ability to reorient volumes (and qform/sform) to LPI orientation

84 lines of code changed in 2 files:

justin 2011-09-05 21:45 Rev.: 2294

This change set implements some changes to the mlrImageHeader. Namely that qform_cdoe and sform_code are dropped = qform is always the xform to the magnet coordinates and sform is always the xform to the canonical magnet coordinates if they exist. Also rationalizing other fields like talInfo (contains AC,PC, etc) and fixing calling programs to use these conventions

167 lines of code changed in 9 files:

justin 2011-09-05 20:26 Rev.: 2293

Saving and loading of qform/sform info in sdt files

21 lines of code changed in 2 files:

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

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

110 lines of code changed in 7 files:

justin 2011-09-05 16:53 Rev.: 2291

Fixing up reading / writing complex data

209 lines of code changed in 2 files:

justin 2011-09-05 12:02 Rev.: 2290

Fixes an off by one error with the alignment. The originOffset (number in pixels) between center of volume to 1st voxel did not have to have a half pixel offset - though conceptually that makes more sense to me. But clearly looking at the actual alignments not adding the alignment is correct

8 lines of code changed in 1 file:

justin 2011-09-04 23:08 Rev.: 2289

Closes controls panel when close button is hit

2 lines of code changed in 1 file:

justin 2011-09-04 23:08 Rev.: 2288

Little function to close an open mrParamsDialog

22 lines of code changed in 1 file:

justin 2011-09-04 22:59 Rev.: 2287

Allows mlrImageHeaderDisp to take arguments in the same style as mlrImageLoad (i.e. you can pass a filename or view or whatever).

78 lines of code changed in 3 files:

justin 2011-09-04 22:46 Rev.: 2286

Only display qform/sform if they are valid

8 lines of code changed in 1 file:

justin 2011-09-04 22:43 Rev.: 2285

Spliting out mlrImageHeaderDisp which can display the mlrImage header

92 lines of code changed in 2 files:

justin 2011-09-04 22:25 Rev.: 2284

Adding mlrImageSave and mlrImageHeaderSave which saves mlrImage data and header structures with an underlying nifti and matlab file (base structure)

155 lines of code changed in 6 files:

justin 2011-09-04 22:24 Rev.: 2283

Minor, remove ver output of fileparts to avoid warning

2 lines of code changed in 2 files:

justin 2011-09-04 17:03 Rev.: 2282

0 lines of code changed in 1 file:

justin 2011-09-04 17:02 Rev.: 2281

This change set adds the ability to select files from input arguments in various ways - identical for mlrImageLoad/mlrImageLoadHeader/mlrVol. You can select by filename, or type canonical or . to put up a dialog box for selecting a file, or pass in a data matrix plus optionally a header, etc. See mlrImageParseArgs for details

490 lines of code changed in 8 files:

justin 2011-09-04 17:00 Rev.: 2280

Check for valid group when getting tseriespath

6 lines of code changed in 1 file:

justin 2011-09-03 00:18 Rev.: 2279

Fix for displaying aligned images in which one of them does not have a xform

25 lines of code changed in 2 files:

justin 2011-09-02 23:34 Rev.: 2278

Fixing small bug in which displayInterpolated interacted strangely with toggling overlay

9 lines of code changed in 1 file:

justin 2011-09-02 23:32 Rev.: 2277

Adding readsdt
Checking for unprocessed epi files

263 lines of code changed in 3 files:

justin 2011-09-02 22:39 Rev.: 2276

fid2xform now works close to correct for epi images.
A few display bug fixes for mlrVol

19 lines of code changed in 2 files:

justin 2011-09-02 17:21 Rev.: 2274

getfidk can now read the epi files again.
mlrVol can display complex data

100 lines of code changed in 2 files:

justin 2011-09-02 15:06 Rev.: 2273

Worked a bit on reading fdf and the orientation info in the agilant created header. This is not quite correct yet.

173 lines of code changed in 6 files:

justin 2011-09-02 14:08 Rev.: 2272

Adding my num2str routine

176 lines of code changed in 1 file:

justin 2011-09-02 11:13 Rev.: 2271

Restructuring code by moving functions around and adding line headers to make things better organized - no major changes to functionality

742 lines of code changed in 1 file:

justin 2011-09-02 00:46 Rev.: 2270

Making warning about matlab version a one-time warning

1 lines of code changed in 1 file:

justin 2011-09-02 00:45 Rev.: 2269

Minor, handling of bad open file better

4 lines of code changed in 1 file:

justin 2011-09-02 00:44 Rev.: 2268

Fixing a few minor things - disppercent when reoredering data, handling of non-image files with sensible error

8 lines of code changed in 3 files:

justin 2011-09-01 23:56 Rev.: 2267

Minor, setting default alpha value to be 0.2

1 lines of code changed in 1 file:

justin 2011-09-01 23:56 Rev.: 2266

Unprocessed files did not have pss set correctly, so we now recompute it. THis seems to fix xforms for 3D and 2D anatomy data.

13 lines of code changed in 1 file:

justin 2011-09-01 21:01 Rev.: 2263

Was using the wrong axis in prepareImageForDisplay when displaying aligned volume

10 lines of code changed in 1 file:

justin 2011-09-01 20:20 Rev.: 2262

Flipping UD and LR of xform - this will now produce different results than before.

1 lines of code changed in 1 file:

August 2011 »

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