updates 2016-10 October-December

ASL preprocessing now generates mean of raw images in T1 space ("t1rmean..."); this could be used for drawwing SUIT VOI's.
Fixed some issues in stats GUI.

Added error information for FIRST in registration stage, as getting errors (if has error will display info in command window).

Fixed bug in basic stats whereby covariates were not corrected added to design matrix
Worked on multi-modality VOI analyses, not finished yet

Tweaked ASL - had temporal filtering bug. If this caused a crash, overwrite files with option in ASL

CSPM database link: An error was being thrwon when connecting to the USyd network db. I updated db_update so that it should not get this error. The only problem it might cause is if there is a computer that has not been used for a while and that has an old database on it (pre 2011-12-20 ) - that's what this was checking for. The network database is fine, but it returns an incorrect name which is what is confusing the issue. (It should call itself 'MariaDB' but it's calling itself "MySQL.") However, my most recent won't affect you or any of the current CSPM users.
ASL: Can specify blood T1 relaxation time - not tested.
Option to Export and Import subject from database. Will not do covariates, only studies and basic infor.

Utility to change project paths, and to change SPM.mat pathnames. THis means we can move the project preprocess folders, including the fMRI 1st level SPM analyses.

The following changes may have issues in MATLAB 2015 and earlier.

Visualization - 3D. Extensive changes.
Visualization - 2D,overlays for multiple blobs working again (stopped working after spm8)
FIR - more tweaks
fMRI RFx - use brain mask from T1 in 1st level models. Should of done this before, probably....
A couple more links from "Visualize study"

FIR/splittask - proprocessing 1st level should not be stable, after some fixes. View study still being worked on.

ASL: finally identified bug - revised ASLtbx takes labeltime and delaytime in s, not ms. Documentation is wrong, but luckily example batch files had seconds. Thanks to Andrew for helping figure this out. (Now have to hope s is in fact correct...)
FIR - dealing with single-challenge, no recovery; allow for 0 length recovery, and avoid contrasts for last 20 scans, as the last (~10?) fail.

PARREC conversion - fixed Philips T2/PD (new T2 sequence). Tested conversion for B1 map (although probably need to store TR times for calculation), and MRA + MAR MIP's.
- Note the Philips PARREC conversion is a complete kludge, but the DICOM files from Philips do something extremely odd.

ASL: added temporal filtering, and implemented ASL-specific motion correction (from ASLtbx).
Tweaked "visualize set".

Fixed a T1 write-normalized problem - for some subjects/studies, the T1 would be re-written every time at the "WRITE NORMALIZED" stage. This was due to a float comparison.
In project, can now indicate that modalities should not be realigned to the T1. The setting applies to an entire study, not just individual scans. This is useful if using a T1 and other scans from separate sessions. By default, this flag is not set.

Started on split task (FIR); currently create contrsts for each scan in task and recovery at 1st level, and an all-effects F contrast. The basic stats analysess this. More to do.
Started with a button to give faster access to the stats/summaries. This works for fMRI and T2R, more to do.

First implementation of SUIT for DTI; has only had minimal testing. Follows similar processing to fMRI and T2R.
Made "voi-gram" script to create series of spectra in same plot. In CSPM, open the file "make_voigram". This replcaes the incorrectly named "make_spectrogram"
Preprocessing - fixed minor bug that would occur with covariates that had symbols in the name