2015-09-30

More to str_format4file adjustments (used in various routines when creating file names); more physiology conversion work

2015-09-29

Correct bug in set creation (Edit/filter), where if studies were loaded from sets, there was an error if a new group was created.
Fixed FreeSurfer bug whereby it would repeat the preprocessing (it was testing for incorrect files and so would always run the prepreocessing).
Working on physiology conversion old-new
Added to str_format4file (used in various routines when creating file names)

2015-09-17

Did more checking for database "Backup" success (called from CSPM GUI) - tidied up the local settings GUIs.

2015-09-16

Added check for database "Backup" (called from CSPM GUI) - checks for empty file (can be incorrect password).

2015-09-15

Minor tweak to local settings (might make test work better)
Working on physiology conversion old-to-new.

2015-09-09

Fixed bug with conversion of some old (2000) GE DICOM files

2015-09-08

Fixed a display message with FreeSurfer preprocessing (said autorecon2 where should have been autorecon3)
Tidied code in spectra (no change in functionality)

2015-09-01

Attempted to fix spectra bug that sometimes occurs related to Excel (was trying to add rectangles, but should not do this).

2015-08-31

Tried fix of error in getting subject info (in Excel) for sets when in filter GUI (error only happens in some circumstances)
Tidied up T1 classification in loading projects (not sets) in "Create set" GUI.
Added a check before unloading existing set (when click load from project or load from set)
Added option to set fMRI bounding box (for normalizing, that is the "w" images).

2015-08-27

Fixed bug in multi-modality analysis where running T2 with no VBM would fail (or select the wrong T2 option).

2015-08-25

Fixed bug that would occasionally come up for single-subject groups during subject file creation.

2015-08-24

CSPM menu - changed label to "Create Sets"
Tidying up physiology in sets. Analysis not done.

2015-08-22 (and 21)

Added a "deselect all" button to analysis GUI - useful if have lots of modalities, especially VOI; will not deselect T1
More physiology development; incomplete.

2015-08-20

T2: T2 map calculation - fixed for spm12 changes
More physiology development (loading WHH, set configuration and filter flags). Incomplete.

2015-08-19

More physiology development (loading WHH, set configuration and filter flags). Incomplete.

2015-08-18

Still working on coreg bug in T2 (only shows up with pre-calculated maps, as in Philips).
Getting color display and VOI creation working (https://osabrainresearch.atlassian.net/wiki/x/QYDBAQ)
Continuing to work on physiology.
Fixed CSPM to work around a MATLAB bug, for RMANOVA creating of timetrends.

2015-08-17

Working on adding physiology to CSPM; tidied up repeated displays of "CON101 done" in some cases when loading projects. Added physiology copy/convert button in project setup.
Fixed bug in FSL FIRST setup stage.
Probably fixed T2 bug during coreg2template stage - spm12 issue.

2015-08-11

Fixed fMRI bias correction bug, that option should work now.

2015-07-30

Working on FreeSurfer, may be ok now.

2015-07-29

Fixed a bug in the fMRI smoothing
Found that there may be a problem with flipping a study and re-running a set analysis - The old unflipped and new flipped might get tangled. Best practice would be to delete the entire set folder, and all preprocess subfolders for that study, if a set has a study that has been flipped since the initial analysis setup.
FreeSurfer - fixed a couple of mistakes, still have a problem.

2015-07-28

Trying to fix a spectra problem; addressing potential spm12 bug. Added option to check for files when VERBOSE turned on.
- Turn on VERBOSE mode (blue button in CSPM and other GUI's - just click any one; see example below) and run again. This will now give you a display of missing files, and a different error message. if you continue to get the same error (which would mean the files are there but unreadable), there will be a link beforehand to the folders where CSPM s trying to read files. You can check those folders and see if the files open in mricro, for example.
Can now create a symmetrical image, which could be used to create symmetrical templates. This needs testing. One image is done at a time.

Trying to fix some FreeSurfer errors, incomplete
Fixed problem whereby some covariates were not loaded (age, sex)
Fixed a bug in the set filter option (came after a recent fix)

2015-07-27

Added default manufacturer option in local settings. CSPM tries to read the from the raw MRI files (DICOM, PAR/REC), but if there is a problem it looks first for the default set in local settings, and if missing or empty, asks the user.

Fixed a FreeSurfer bug.

2015-07-24

Fix spm12 bug for T1 setup (if had more than one T1, the "T1 setup" in the analysis GUI would fail.

Fixed covariates bug: would not correctly add a single covariate value (Subjects GUI => Covariates GUI)

Fixed minor bug where had extra stuff printed to command line when editing/adding subjects from Subjects/Data GUI..

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