These release notes refer to the latest CSPM changes, which are uploaded to Google Drive (help getting files - see SyncBackPro updates July 2022). Sometimes files outside of CSPM are updated; if so, the notes will mention “matlab update”.
MATLAB version: 2022a.
2022-12-15
fmritype - fixed db bug
CSPM startup - db updating with restored database, adjusted for quirky error (“version” table” lost data); this should also be backwards comparible with old versions of database running in recent MATLAB releases.
updated documentation, saved new startup.m file for Sydney - see MATLAB Startup.
Note: requires that CSPM matlab files be in C drive in “matlab” subfolder: C:\matlab (not on D drive for example)
Check to make sure CSPM GUI is on the screen
2022-12-12
DTI - fixed bug that sometimes happened running older sets; added command window info for normalizing DTI step
1-D - Nicer 2-group Box plots
2022-12-06
Preprocessing - fix bug with older sets
SetsGUI - should update now - very odd Google Drive error - an updated cspm_sets_config_App.mapp file was uploaded, and is listed as recent (Dec 1 2022), but when downloaded it’s an older version! (Jul 7 2022). (Fixed by uploading newer file.)
Subject delete - code changes to be compatible with recent MATLAB releases
2022-11-30
Set configuration - made some tweaks to GUI, may work better in <4k screens
Subject delete - some code changes to make compatible with current MATLAB, not tested
Projects - Fixed delete study, created App version of configure (being tested)
2022-11-28
rsMRI new measure - Display Results updated (guide moved to App), should work for correlation map measures.
2022-11-18
fMRI - added checks for corrupted files in matching to T1 space, realignment - now if mean is corrupted, checks for previous-step (files used to create mean - detrened, bias corrected, etc.)
2022-11-17
fMRI - added checks for corrupted files in matching to T1 space, realignment
2022-11-07
fMRI connectivity - fixed (one) bug
2022-11-06
fMRI connectivity - may have fixed bug
Set “1D” files created, change set stats GUI to remove “metric” since this is in 1D results
2022-11-01
Sets config - fixed multi-project selection bug
2022-10-28
DICOM convert - fixed (hopefully) bug in pre-2022 conversion
2022-10-17
Pubmed (matlab update) - updated for 2022a/b, and for French spelling of June (“juin”)
2022-10-16
Grayplots - added physiology, options, tidying display, tidying code (ongoing)
CSPM GUI - renamed Stats to 1-D stats…. to distinguish from MRI stats
2022-10-07
Grayplots - more progress on individual display options
Basic stats - smoothed out process of reloading when making parameter changes.
2022-10-06
Basic stats - fixed startup bug
Basic stats - fixed 2 group labelling issues, fixed problem with boxplot group labelling, added bar/box figure scaling (to make consistent sizes for export).
2022-10-05
Basic stats - correlation works with 1 group; disabled some options that are not used.
2022-10-04
Basic stats - save time making tables for papers, look at means and correlations quickly. Will expand this tool but it's a start
2022-10-03
4D files - fixed a quirky bug with 3D-to-4D conversion, including the one in lmgs (did not affect 3D processing)
2022-09-30
Analysis GUI - ready/running lamp
Phys - fixed error
fMRI+phys - fixed bugs - large file saving, correlation maps
2022-09-29
DTI - fixed errors related to CAT
fMRI - fixed recent bug with voxel size going to NaN
fMRI - fixed issue where CAT would lead to re-writing t1-space normalization
DTI - separate match-to-t1 into CAT subfolder
Analysis - tweaking table; option to skip BIDS, protocol tables easier to read, checking for some errors
View metric study - fixed bug
2022-09-28
DICOM convert - fixed a bug that sometimes happened; added search for *.dcm files in subfolders
Analysis protocols - fixed some bugs; might be working!
2022-09-26
Linear detrending - fixed bug introduced yesterday
2022-09-25
Linear detrending - if memory is available, will load volumes, and write as volumes (instead of slices). Might speed up, and reduce chance of network error.
2022-09-23
DICOM convert: added new option that works with 2022 7T and Philips data https://osabrainresearch.atlassian.net/wiki/x/AYCLdw
Protocols - can go from fMRI through to grayplots in new stats GUI; code being tidied still.
Phys import - in progress
First testing ith MATLAB 2022b (release just a few days ago)
2022-09-21
Project - delete study fixed
Coreg - fixed nifti_folder error; changes to GUI
Analysis protocols - added for T1, VBM and fMRI
DICOM convert - added option to use MRIcroGL (still being tested); testing with Melbourne and Neura scans
2022-09-16
Coreg - option to view coregistered files in Projects and Sets GUIs
Project GUI - revamped to fit in screen and be resizeable
2022-09-15
Coreg - check for cursor not at origin (a tricky sneaky problem otherwise)
Tidied Projects GUI - others will need similar fixing to deal with new MATLAB graphics
grayplots - more options and fine tuning
2022-09-13
Fixed study delete bug, check paths bug; tidied check file paths
Grayplots for fMRI - getting closer
Fixed DPARFS subject load bug (sync matlab files, not just CSPM)
Added option to correct datapath for studies (path to raw data)
T1 - added warning if missing files (used to only be with VERBOSE)
2022-09-12
Started on gray plots (new Stats GUI)
Started on checking for missing paths (not complete)
2022-09-10
fMRI - local processing for writing to warped - small speed difference on UCLA network; tested for normalization, does not make much of a speed difference on UCLA network
PPI - removed matlab warning
2022-09-09
PPI - may have fixed bug at end of processing
Preclinical - creates masks
fMRI - slice timing does local processing.
Sets GUI - save set button less likely to disappear on some screens
2022-09-07
fMRI + phys - some bug fixes.
2022-08-29
Physiology and fMRI - extensive under-the-hood changes to physiology and physiology with fMRI.
Bug fixes
export_fig updated
2022-08-09
Projects GUI - updates and bug fixes; working on physiology side of things.
2022-08-08
Updated Projects GUI; manual coreg now works directly; subjects info and mri/study info now work
phys types - fixed GUI
...
2022-08-05
fmri types - fixed GUI
Cosmetic changes to some GUI’s
Tidied some underlying code
2022-08-01
Preclinical - does DBM files (Jacobian) - should be tested
...
2022-07-22
Substantial and extensive changes!
CAT12:
The analysis will now run CAT12 segmentation and normalization; in the future, this will allow us to analyze surface files from CSPM
The normalization works for some T1 scans that DARTEL fails on (in HCP in particular)
There is now a separate normalization (indicated by “C”) for DTI, fMRI, T2 and VBM
...
fMRI analyses - does summary files of 1st level contrasts to more easily detect problems
There may be banding in some fMRI 1st level contrast maps…
2022-07-19
Fixed manual coreg bug
2022-07-15
Image information - Added option to show custom thresholded volumes. Example setting custom flags.
...
>> flags.vox_below_th = 0.25;
>> im_info(P,flags)
2022-07-08
Bug fixes for Preprocess, Analysis GUI
2022-07-07
Fixed problems with Analysis GUI
2022-07-05
Note: google drive issues, might be slower. May need to restart, may need to re-authorize connection.
Updated: CAT12 toolbox, option in T1 analysis may be working….
Tweaked - DICOM rename/convert (moves to center, updated for 2022a)
Fixed - sometimes-error n analysis GUI start; goes to middle of screen (used to try to remember last position; puts ID in window name)
Fixed - preprocess opened old stats GUI on finishing
Disabled r to z button (does not work, not needed)
Set stats - moves to window center (avoids off-screen)
New fun tool - search pubmed and create word cloud (and a few other things
2022-06-17
Fixed fix below!
2022-06-16
MATLAB 2022a problem - DPARFSA - probably will be several more of these
Tweaked fMRI connectivity GUI’s
2022-06-03
Fixed PPI problem
...
2022-05-24
Updating physiology - study import, event save, event creation from channel
2022-05-16
Image info updated
...
Working on physiology
2022-03-27
pc - T2 implemented, fixed some errors
2022-03-24
pc - should do VBM and DTI without errors
2022-03-22
pc - says if missing some DTI files
2022-03-21
pc - now might do DTI….
2022-03-18
pc - might do DTI….
2022-03-05
pc - smoothing, copy to stats folder, anatomical check no longer re-runs
2022-03-02
pc - fixed template bug
2022-03-01
pc - added check-reg option (make sure have stats folder)
preclinical - starts with coreg, does old norm (unified).
2022-02-27
T1, stats - fixed missing TIV, BV etc.
2022-02-22
CAT12 files updated (will take a while to download)
DRIFTER: modified to run MUCH faster
DRIFTER (other functions in the future): option to copy files to local computer to speed processing (and avoind read/write errors)
...
Stats GUI, fixed SPM bugs
2022-02-21
Stats GUI, fMRI VOI connectivities - fixed bugs, adjusted for older sets
2022-02-17
Preclinical - does coreg (does it work…?)
2022-02-16
Preclinical - fixed scaling (maybe) - delete all existing.
2022-02-15
Fixed Stats GUI bug running SPM’s
Preclinical testing
2022-02-14
Fixed error in analysis GUI with DTI
Fixed (hopefully!) VBM SUIT bug
Freesurfer tweaks
2022-02-07
Tweaks to project info
2022-02-06
Added option to see a subjects project information - where the a raw data studies are organized in projects (opens in Excel)
Fixed quirk in Analysis GUI where settings changed would not “take” (but they would be correct on reload of GUI)
Many changes to code - working with matlab transition to new gui’s
Fixed fMRI physiology vector bug
Fixed FSL bug
Freesurfer: will redo processing if files are 2021 or earlier, as this was in earlier version of freesurfer (current 7.2, old 6.0)
2022-02-01
Fixed Subjects GUI bug (must have been there since Jan…?)
2022-01-31
LOTS of changes to accommodate recent new code
T1 create ref - added info
Preprocess GUI - tidied
Fixed another mouse bug (from CAT12 changes)
2022-01-28
Changed default cat12 to off (mistakenly on in recent ~1 week analysis GUI)
Fixed mouse bug
Tweaked freesurfer, hopefully fixed bug
2022-01-26
Fixed a neveroverwrite bug for T1 ref create
Added extra check in mouse (file copying)
2022-01-25
Analysis GUI: fixed initialization error
CAT12: started coding; incomplete
FreeSurfer: commands that work with 7.2 (incomplete)