updates 2015 October - November

FIRST stats - formatting Excel file (added comment to use Ctrl^PgUp and Ctrl^PgDown to shift between worksheets), gives list of significant results.
ASL in CSPM - first pass at getting this to work for resting state CBF maps (not fASL); need to set parameters in a text file (opens when Preprocessing button clicked and ASL is selected).
Tidied up FIRST stats - clustere/m do not produce uncorrected p-value files
ASL GUI - added option to skip smoothing, added option for silent processing (no messages in command window)
Corrected mistake in FIRST commands to run design vertex and randomise analyess
Fixed inconsistency in local settings Ping; added some defaults.
Bug fixes on ASL, FIRST stats running.

Physiology: have initial preprocessing working (to figure creation). Only works for already loaded data, but it is a first step. Will create import tools in the future.

Subject info working with phys data.
Added copy/convert button in project setup GUI (since if path is ok in subjects GUI, don't need to select path)
Tidied fmritype and physchallengetype GUI's for MATLAB 2015b
Conversion tool for old hd2000 physiology
Removed repeat option from mir/phys recording level; in the future repeats (longitudinal) will be at the study level (not implemented yet)
tidied images files GUI
added some database tools (db_dt tablename, db_st to show tables)
CSPM start - sped up by removing what I think is an unnecessary command (spm_jobman('initcfg'))

Add FSL FIRST automatic analysis for manually created designs; button in stats window. Runs all vertex and randomise analyses, and gets fstat1 p values into an Excel file.
Corrected mistake in ASL gui, added "ms" labels.
Option to extract image intensities and display them - from Image menu in CSPM
Fixed recently-introduced PARREC conversion bug

Set copy files for project to check for newer rawimages
FSL FIRST text files improved (for randomise commands - have F and t tests separate)
DICOM convert fixed for Philips DICOM files

Fixed basic stats GUI for latest MATLAB (added resize option), tweaked local settings GUI.
Fixed T1 conversion for FSL to check for excessive values - since FSL needs int16, maximum value set to 2^15.
Tweak to Analyze set GUI

Tweaked settings on CSPM and local settings GUIs (also changes to phs convert, but that's not relevant to most people)
Corrected set filter/create groups GUI, added resize option
Correct Local settings GUI
Correct error introduced a day or two ago which caused any database connections to fail (and freeze matlab)
Added option to check converted files for very large intensity ranges; this arose from ~12 Sydney subjects with T1's having intensities in the ~1,000,000 range, as opposed to the normal ~1,000 range. This will only check single scans (not fMRI, T2)
Added ASL-only overwrite option to ASL GUI.

Added GUI to ASL toolbox ("ASLtbx"); access via CSPM ASL menu. This works with Philips ASL files. Will probably need some tweaking.

Fixed bug that would arise in dicom rename/convert when a patient id had a "." in it. Tidied the GUI a little.
Loading sets now only loads studies in set, not all subjects in projects - very useful for subsets of large projects.

DTI - switched from eval3 (3rd eigenvalue of tensor) to free water fraction estimate (FW)
Corrected mistake that crept in with previous changes, leading to incorrect location of "dw_realign" folder
Deleted a couple of unused files
Fixed error with non-SUIT introduced in previous updates
GUI's tidied and fixed: Project setup, imagefiles, view setup, project configuration
Backend database design and CSPM software altered so that raw data path is only recorded in study table; should be no user differences, but design is simplified
Analysis GUI: removed options to select specific DTI indices; all will be calculated
(from earlier, but noted: 3rd eigenvalue included as a variable, as a precursor to Free Water measure)

Project configuration: added confirmation to delete MRI (previously one click would delete, so could accidentally delete an MRI)
Project configuration: corrected GUI layout bug
Save column width option fixed for 2014b onwards
Probably fixed bug where occasional subjects repeat T1 preprocessing every time (this occurred when a subject had more than one T1 scan, with different resolutions, and with the highest resolution scan not being the first in the list).
DTI processing in SPM12 with more than two scans now works
Corrected "orphan" mri's giving "Study missing" errors; errors will show once, then not repeat (see command window for studies affected)
Saved batch jobs for creating fMRI designs will now open in SPM12 Batch manager (other modalities may still need fixing)

Correct analysis and set analyze GUI's so they view properly on screen (problems with ~4k laptop, and other computers)
Corrected SUIT bug whereby smoothing would get labelled with whole-brain smoothing value, not suit smoothing value.
Adjusted FIRST randomise example in text file to be runable.
Tweaked Linux setup to catch when subjects4freesurfer folder not correctly set up.
Adjust DICOM conversion to work with Skyra DTI files
Set database defaults to correct handling of "null" (read as empty, not as the word "null") in cspm_defaults

Discovered very odd issue that came up with converting physiology: ODBC connection showed more rows in some tables (mrilink) than via JDBC connection.

Fixed bug with DTI run-one in SPM12 (cspm_dti_coreg.m, cspm_dti_b0computations.m).
dti run-one prints pdf images (still problem finishing mrVista processing due to obsolete language)

Fixed T2R SUIT issue with switch smoothed and non-smoothed images in multi-modality analysis

ASL - more adjustments do deal with Philip functional ASL (not ready to run in CSPM)