Updates 2023
- Paul Macey (admin)
2023-12-15
DTI info - a lot of tidying, including looping through DTI\raw subfolders
2023-12-15
DTI info - a lot of tidying, including looping through DTI\raw subfolders
To test subfolders, search for DTI info files and delete them (see 2nd snapshot). If preprcessing is in those folders, the dwmean and dwstdev will mess things up (since they don’t have DTI directions or b -values)_
2023-12-08
Preclinical - fMRI for > 1 study bug fix
2023-12-05
Preclinical - one bug fixed
2023-12-04
Preclinical - fMRI group stats, files copied
2023-12-01
Rename nift files - basic tool (need to edit m-file and run)
2023-11-17
PPI - some tweaks to make it run more smoothly, prepare for multi-measure
2023-10-30
Preclinical - probably runs now, fixed bug for more than one VBM
2023-10-29
Timetrends - “RMANOVA” option, if not selected will not try to run SAS.
2023-10-25
Set stats SPM - may have fixed bug with decimal places in measure name.
2023-10-18
fMRI - fixed rare bug in 1st level boxcar; if a project path had been changed, and the old path was not available on the computer running CSPM, the old incorrect path would nevertheless be “remembered”.
2023-10-17
Database - updated utilities to change paths for raw and project (preproceessed) data
2023-10-09
Display results - fixed SPM cluster bug
2023-10-05
sets GUI - tweaked odd case of missing study, gives command line info instead of error box
sets GUI - fixed bug on update folder
sets GUI - fixed bug on gui startup
2023-09-24
preclinical - fMRI individual preprocessing implemented (1st pass; probably needs debugging); fMRI sets not implemented yet
2023-09-20
preclinical - tidied up VBM - can select options for types (VBM tab), will remember last selection
2023-09-17
preclinical - should work for VBM, but not thoroughly tested
2023-08-25
BIDS setup - added .bidsignore, should create folder ok.
fMRI correlation maps with VOI timetrend - now VOI x measure button
2023-08-20
TIV, brain volume etc. now added to variables available for analysis (basic stats, 1D files). Note: the 1D excel files will be updated each time the preprocessing is run, so that values will change according to the most recent T1 analysis.
fMRI VOI connectivity by measure - basics are working; call from Set Stats GUI
2023-08-19
Set Preprocess GUI - updated, filtering works
Other changes mid-way for VOI-VOI by measure, preclinical
2023-08-17
Preclinical - updates
2023-08-16
Preclinical - new version - process up to coreg should be working. Full preprocessing is not
2023-08-15
Preclinical - more in process changes - NOT WORKING - do not update if you’re using preclinical.
DTI run one - fixed bug. Note that needs ghostscript to create figures.
2023-08-14
Preclinical - more in process changes - NOT WORKING - do not update if you’re using preclinical.
Tweaks to DTI code
2023-08-10
Preclinical - in process changes - NOT WORKING - do not update if you’re using preclinical
Network testing - should be functioning version now
2023-08-09
Network testing - version 1 of testing tool
2023-06-27
fMRI VOI timetrends - fixed bug; couple of updates during day
2023-06-23
Preprocess - fixed bug that sometimes came up (previous show-archive setting)
Load set - fixed bug with very large exam numbers
2023-06-22
DTI - added one check for missing files at realignment/eddy correct stage; might identify problem that otherwise shows up in next step (b0 calculations)
2023-06-01
ASL - fixed (hopefully) bug that was not fixed earlier
Preclinical - incomplete fMRI
2023-05-18
BIDS tweak
DICOM conversion for DTI - added adjustment that recognizes when DTI series includes derived files (like ADC), which sometimes happens with Philips data (Neura), for example. The Siemens approach is to store derived files as a separate series; having one series containing both raw data and derived files is confusing.
Here is the option shown in the Import GUI from MRIcroGL (that runs dcm2nii)
2023-05-16
DTI- reverted back
2023-05-12
DTI- may have fixed eddy current correct bug that caused error; however, not sure if this is working as expected even if not crashing
2023-05-11
fMRI - added a check for 4D files (but only for slice-timing…)
matlab update; DTI - fix a bug for b = 10, should now work with b0 max as set in Analysis GUI (not editable yet, defaulting to b = 30 for Bruker)
2023-05-02
DTI - works with 10 min b-value (for b0 corrections)
2023-05-01
Preclinical - fixed bug that occured when excluding T2
ASL - fixed bug introduced a few weeks ago
Bruker T2* - fixed bug from yesterday (may'd it work)
2023-04-30
Bruker T2* - will crash somewhere different!
1D stats - background tweaks, in process (error with Factor)
BIDS - in process
2023-04-21
SUIT - NEVEROVERWRITE works for T1 preprocessing
Analysis GUI - removed legacy T1 coreg option (that used “manual2mni” folders)
2023-04-20
1D stats - fixed color bug
BIDS - changes in Project GUI, not working yet.
2023-04-17
T1 jacobian - NEVEROVERWRITE now works
T1 ref native space reslice - fixed bug
Phys - tweaks to GUI
BIDS - not yet working - testing for fmriprep
2023-03-27
T1 ref native space reslice - now reslices onto local temp folder, then moves back to network drive. 1) Might fix some Sydney network issues; 2) should make it faster.
2023-03-14
preclinical - added custom scale option
project add - reverted to datainsert from sqlwrite (for Sydney db)
2023-03-09
DICOM convert - added help
2023-03-05
DTI: added app to remove images with specified b-values
2023-02-16
Added SNR, and fixed stdev bug.
For SNR, either select mean & stdev, or select series and it will calculate mean and stdev
2023-01-23
Project add study - fixed bug
2023-01-13
Sydney db - workarounds for db errors, in projects that subjects and projects will work; tables seem to be OK, database itself is buggy
2023-01-09
Sydney db - identified consistent errors; did workarounds so that subjects and projects will work; tables seem to be OK, database itself is buggy
Improved code for subjects and projects GUIs