2015-11-24
- 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.
2015-11-23
- Added ASL option to skip T1 coregistration and realign within-series.
- Bug fixes of FIRST, database loading.
- Image intensity info (CSPM Image menu) can now read nii.gz files.
2015-11-22
- 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.
2015-11-21
- 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'))
2015-11-20
- 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
2015-11-19
- 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
2015-11-18
- 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
2015-11-17
- 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.
2015-11-16
- Added GUI to ASL toolbox ("ASLtbx"); access via CSPM ASL menu. This works with Philips ASL files. Will probably need some tweaking.
...
- Replaced old ALStbx in CSPM subfolder with most recent version
2015-11-15
- 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.
2015-11-14
- 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)
2015-11-13
- 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)
2015-11-12 (and few days earlier)
- 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
2015-10-20
- Minor changes to str_format for physiology conversion.
2015-10-18
- Discovered very odd issue that came up with converting physiology: ODBC connection showed more rows in some tables (mrilink) than via JDBC connection.
2015-10-15
- 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)
2015-10-14
- Fixed T2R SUIT issue with switch smoothed and non-smoothed images in multi-modality analysis
2015-10-03
- ASL - more adjustments do deal with Philip functional ASL (not ready to run in CSPM)
2015-10-02
- ASL - tweak to Philips to start setting up challenge (functional) ASL types
- Added T2 SUIT option. Should work perfectly since it's been tested once.
- Continuing on physiology conversion.