Philip Cook committed [4194e9]

ENH: Check quaternion validity and correct for precision errors

Philip Cook committed [8787dd]

Test output including new conmat functionality

Philip Cook committed [d3b8d9]

ENH: Allow SD as a tract stat

Camino released /camino-code-1c4ef77615d103d43adcff6c79b72d0bbdac0897.zip

Philip Cook committed [1e57b0]

ENH: Allow conmat to count longest paths.

Philip Cook committed [1c4ef7]

Tests for longest path endpoints

Philip Cook committed [b04ae0]

BUG: bitpix set incorrectly for RGB images, doesn't bother ITK but fixing anyway

Matt G Hall committed [fd22f5]

removed stray CORBA import which was causing compile issues with Java 9+

Philip Cook committed [37ef03]

Somehow lost the code that allowed headers in conmat label definitions. Re-adding it

Philip Cook committed [e2b21c]

Adding an option to conmat to output the graph nodes

Philip Cook committed [87b101]

Allow -unweightedb in estimatesnr

Philip Cook committed [6bb25a]

Make -bscale 1 the default, which is what most DTI users will want

Camino released /camino-code-a844005b39c2fc7fd5d33c6af977e44248de42cd.zip

Philip Cook committed [a84400]

ENH: eig2nii converts dteig output to nii

Philip Cook committed [af55b0]

ENH: Allow non-zero unweighted measurements for dtspd

Phil COOK committed [746cf9]

Another attempt to fix bigbass script test problems

Phil COOK committed [477e5a]

Reverting bigbass test output - not sure why it changed

Phil COOK committed [fef420]

Automated test update from nightly build script

Matt G Hall committed [89d3c1]

opps! forgot that this needs to happen from trajfiles as well. Added same machinery to signal generation from trajfiles as well.

Matt G Hall committed [97266c]

minor changes and small catches plus some generalised tidying up.

Matt G Hall committed [440ff5]

enhanced signal generation code which generated real, imaginary, magnitude, phase information with combination controlled by front end specification. Output is scalar unless COMPLEX or MAGNPHASE options are chosen, in which case this builds 2N scalars with a pair per line in the scheme file as {real, imag} or {magn, phase} respectively. This is draft and untested.

Matt G Hall committed [847743]

top-level machinery and calculation flags. not functional yet.

Philip Cook committed [e3171d]

Updating doc

Philip Cook committed [3d42fe]

Document cone of uncertainty output for orientbiasmap

Matt G Hall committed [bd68a2]

remove the moduli from AgnosticScan's phaseshift accumulator to see if this was causing problems

Matt G Hall committed [a4e1df]

remove the moduli from AgnosticScan's phaseshift accumulator to see if this was causing problems

Philip Cook committed [892293]

Standardize residuals

Matt G Hall committed [f9f750]

added logging message to check dot product timestep case is being caught successfully

Philip Cook committed [68464b]

Increase I/O buffering

Philip Cook committed [3b644b]

WIP on dtspd command. Also did some I/O speed tinkering

Philip Cook committed [68b018]

dtspd command implemented

Philip Cook committed [60e35d]

Merge branch 'master' of ssh://git.code.sf.net/p/camino/code into dtiQC

Philip Cook committed [f71354]

Output additional stuff from orientbiasmap

Philip Cook committed [0b3002]

Merge remote-tracking branch 'origin/master' into dtiQC

Philip Cook committed [613237]

Almost complete first pass

Matt G Hall committed [7b90f4]

annoying bug which was killing the exchange statistics -- wasn't breaking out of the loop which checks exchange probs correctly which meant that everyone ended up stuck in the last fluid. should be fixed now.

Phil COOK committed [a84f13]

Automated test update from nightly build script

Philip Cook committed [8dca6e]

Working on fixing negative eigenvalues and other QC output. Might also try iRESTORE

Philip Cook committed [fada9b]

Update test to deal with new default bscale = 1 for fsl2scheme

Matt G Hall committed [091948]

found a stupid bug. All RNGs used to exchange between fluids all had the same seed, which meant that either all the spins exhcange or none of them do. Added a seed offset to each one, and we now have different exchange trajectories for different spins. There was also a problem with the stats, whereby counters were incremented at every timestep regardless of an exchange event or not. This is now also fixed.

Matt G Hall committed [d763b1]

added output of raw exchange statistics to text files after multifluid simulations. exhcanging walkers count their exchange events and output this and their mean residence times at the end of dynamics.

Matt G Hall committed [1d78ed]

added an optimisation to the gradient impulse calculation from GradientWaveform_Schemes which takes advantage of a special case where the umber of updates in the dynamics is the same as the number of blocks in the waveform scheme. Underthese circumstances the phase shift for a spin reduces to the dot product of the trajectory and the genwave. This case is now explicitly checked for as the scheme file is parsed. There's a final flag introduced into the GradientWaveform_Scheme object which diff...

Philip Cook committed [1886d5]

Make -bscale 1 the default for fsl2scheme, as m...

Matt G Hall committed [b8b13b]

fixed problem with all multifluid walkers execu...

Matt G Hall committed [f36b42]

removed debug messages

Matt G Hall committed [8f5cf2]

changes to stepgen factory to allow non-singlet...

Matt G Hall committed [d9c7eb]

further initialisation fix.

Matt G Hall committed [391e4c]

bugfix in multiple diffusivity initialisation

Matt G Hall committed [2076e7]

fixed initialisation issue in multifluids where...

Matt G Hall committed [a10f50]

small bugfix on command line

Matt G Hall committed [a1e7b2]

added commandline specification of initial walk...

Matt G Hall committed [b3cc73]

fit draft of exchanging walkers, including comm...

Matt G Hall committed [a80059]

Define javac variable in Makefile, needed to pa...

Matt G Hall committed [90e4db]

Merge branch 'master' of ssh://git.code.sf.net/...

Matt G Hall committed [461aff]

undoing previous accidental commit to master br...

Matt G Hall committed [fc6566]

first draft of multi-fluid exchanging walkers. ...

Philip Cook committed [e822f2]

Define javac variable in Makefile, needed to pa...

Camino released /camino-code-9cf8bef17561e88d730df3bc6a8bc111ed1d93aa.zip

Philip Cook committed [9cf8be]

Merge remote branch 'origin/master'

Philip Cook committed [aca240]

BUG: image extension error when writing .nii fi...

Camino released /camino-code-be29107b79b741fea838a50cc419700dd79536bf.zip

Philip Cook committed [be2910]

DOC: Correct averagedwi example usage

Philip Cook committed [1033fa]

BUG: SteTan scheme file should be all SI units

Philip Cook committed [3341ea]

Merge remote-tracking branch 'origin/master'

Matt G Hall committed [f17500]

minor bug fix in simulation

Philip Cook committed [91291d]

BUG: Fix run-time error when computing conmat w...

Philip Cook committed [1d5451]

conmat - endpoints were always applied. This is...

Philip Cook committed [9074d5]

Merge branch 'master' of ssh://git.code.sf.net/...

Philip Cook committed [7c400e]

Use NIFTI qforms even if the code is 4 (needed ...

Phil COOK committed [e7ccf6]

Automated test update from nightly build script

Philip Cook committed [5a8baf]

ENH: Zero out gradients in fsl2scheme if b-valu...

Philip Cook committed [f1969d]

Merge remote-tracking branch 'origin/master'

Phil COOK committed [40093e]

Automated test update from nightly build script

Camino released /camino-code-d64fe361776a8ee02a41f13e6b180ddd574f8882.zip

Philip Cook committed [d64fe3]

Adding files to go with previous commits

Philip Cook committed [f93fee]

ENH: New code to subset data

Philip Cook committed [f23c6a]

ENH: Testing files for new code

Philip Cook committed [e2df9c]

Merge remote-tracking branch 'origin/master'

Philip Cook committed [7525a0]

BUG: Linear fit failures could cause residual /...

Camino released /camino-code-242333329b834f198017f6c97f81335072e2d59b.zip

Phil COOK committed [242333]

Automated test update from nightly build script

Philip Cook committed [63b3d0]

Avoid introducing a requirement for Java 8 by u...

Philip Cook committed [869880]

Test and improve averagedwi program

Philip Cook committed [163748]

ENH: Average DWI, select shells to average over

Philip Cook committed [f01240]

DOC: Man pages for functionality to be developed

Matt Hall committed [4d0a5b]

nested cylinders on distributed substrates

Matt Hall committed [1b94c0]

Added nested cylinders with specified depth, ad...

Phil COOK committed [b6b20f]

Automated test update from nightly build script

Philip Cook committed [4221ef]

BUG: nii2dt missing the java call to test for a...

Philip Cook committed [770f62]

Merge remote-tracking branch 'origin/master' in...

Philip Cook committed [1b8fcc]

ENH: Bedpost tracking, now with docs and tests

Philip Cook committed [4cfc82]

WIP: Bedpost tracking. Need to test against pro...

Phil COOK committed [0f2de6]

Automated test update from nightly build script

Philip Cook committed [eb05fc]

BUG: Update tracking results.

Philip Cook committed [4a5811]

BUG: New script test to go with new tracking re...

Philip Cook committed [f32d4d]

Merge remote-tracking branch 'origin/master' in...

Philip Cook committed [de10c3]

BUG: Make test results for SH norm moment consi...

Philip Cook committed [d43a3d]

ENH: Add an option to output tracts in voxel sp...

Philip Cook committed [252deb]

ENH: Bedpost dyad tracking appears to work and ...

Philip Cook committed [5e55e8]

WIP: Bedpostx dyad tracking + probabilistic sup...