updates 2015-08 August-September

Owned by Paul Macey (admin)
Last updated: Jan 03, 2016
4 min read
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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