updates 2019-06 to 2020-12
- Paul Macey (admin)
These release notes refer to the latest CSPM changes, which are uploaded to Google Drive.
2020-11-30
fMRI slice timing - extra help messages
Phys - more tweaks to app
2020-11-04
SUIT fMRI new VOI connectivity measure - possibly fixed bug where looked like got masked file in r-values (was actually scaled using same parameters as raw files, which does not work well for r- values; r-values close to 1 in VOI, which is why it looked like it was masked.
2020-11-02
Coreg-to-MNI - fixed rare bug
Protocol GUI - added undo state delete
2020-10-29
SUIT fMRI - possible fix for measure not showing up (no 1st level models created)
Physiology - more progress, not complete
2020-10-20
Stats GUI - had problem, fixed.
2020-10-19
Mouse - more tweaks
Phys - working on app, not complete
2020-10-15
Mouse - mean check reg
Phys - working on app, not complete
2020-10-12
Coreg to MNI - GUI tidied
2020-10-09
mouse progress
physiology viewing additions, part way through
Identified problem with 2020b, can't edit GUIs with normalized font units.
2020-10-05
Project Copy and Coreg - more tidying and error checking
Physiology view study - working on GUI
2020-09-27
Preprocessing - more file checks in case of corrupted files (happens when preprocessing over network drives, especially smoothing and reslicing
Tidied Project Copy and Coreg
Add initial mouse - need matlab, not just CSPM updates
SPM updated to latest version
2020-09-18
fMRI slice timing - file should be placed in nifti not raw data (DICOM. PARREC) folder; temporary fix to look for slicetiming.txt if missing
2020-09-17
PPI - fixing missing smoothing
2020-09-16
PPI - added changed mask threshold from 0.8 to 0.0001 (to work with SUIT images.... check for other problems).
2020-09-14
fMRI - fixed some typos that (probably) caused slice timing to crash
2020-09-11
PPI - tidying code, works with SUIT, tidied display messages, added wiki page.
PPI - working as psychophysiological interactions, not physiophysiological interactions
PPI - uses an F-contrast
2020-09-10
mouse - start (https://osabrainresearch.atlassian.net/wiki/x/CIDIPQ )
File copy for project - added check for file numbers for fMRI (will work as along as fmritype is selected in project)l
2020-09-09
PPI - code set to run through and create new measure (not properly tested)
T1 preprocessing - several extra checks to look for corrupted files.
2020-09-08
Major update: raw DICOM/RPARREC files not copied to project folder
No more apply T1 rotations to other modalities
Manual Coregistration to MNI done from Project GUI (run new app)
HCP import tweaked; still not final.
CSPM - make initial shrinking of SPM optional (check to shrink on startup)
PPI - won't ask for mask file
2020-09-01
PPI - one more fix
2020-08-31
PPI - tweak, may get one step further
2020-08-28
PPI - new GUI from Stats, first pass, may work....
fMRI - SUIT boxcar should work now
HCP import tweaks
CSPM physiology folder tidying
Slice timing reads from Siemens DICOM
2020-08-24
fMRI - if have vector common with boxcar (and hrf is selected), will create 1st-level of SPM condition, not regressor
Basic stats - fixed variable de-selection (had stopped working)
Basic stats - minor UI tweak
HCP import tweaks
2020-07-28
Basic stats - minor bug fixes, formatting changes, tidying display options
Fixed: group diff for desc, display boxplots works properly, plot wrt correlation y axis labels corrected
Added: Bargraphs optional, displays command window warning of missing values
2020-07-27
Fixed new fMRI measure, 2nd level stats.
CSPM - starts with SPM smallified
Basic stats - fixed minor bug
2020-07-16
Updated basic stats - works with 3+ groups, fixed boxplot not display option.
minor tweaks
2020-06-25
Many refinements on basic stats; can do factor subgroups, correlations wrt single variable, has better table formatting for copy-and-paste into Word
2020-06-10
Basic stats: added colors for bar graphs, subfolder save option
Metric - Proprocessing set will create Subjects file if no MRI or phys.
2020-06-16
Fixed vector error (convolve with hrf assumed TR = 1 sec)
More tweaks to basic stats
Metric loading, testing
2020-06-10
More tweaks to basic stats
2020-06-09
Tweaking basic stats - bar graph/boxplot option, tables for copying to Word
Survey load and metric importÂ
2020-05-25
Tided loading metrics from excel
2020-05-21
Adjusted VOI-VOI to work for more than 50 VOI - tested once.
2020-05-16
Minor changes to RMANOVA in Display results - no substantive changes.
2020-05-13
Fixed Display Results for sub-mm resolution data.
2020-05-07
In VOI menu, added option to calculate inter-rater reliabilities. Need files named in set convention.
2020-05-05
May have fixed timetrends for non-boxcar fmritypes.
2020-05-04
Added option to read effect from SAS RMANOVA models, fixed Excel export to work with MATLAB strings.
2020-04-28
Fixed read timetrend bug introduced last week.
2020-04-22
Fixed slice timing recent bug for non-custom settings.
2020-04-21
Fixed RMANOVA covariate bug.
2020-04-20
Updated loading of timetrends (Display functional) to allow for much faster saving/reloading, and a little bit faster loading.
2020-04-19
RMANOVA - have option to run RMANOVA with any covariate (needs SAS)
Set stats - can update covariates without re-running preprocessing
Covariates from physiology - can create mean/media/iqr/std from physiology (only if linked with MRI at present)
2020-04-15
CSPM Buttons to scale SPM window down and move to corners - need to update two SPM files as well as CSPM.
2020-04-08
VOI connectivity bug fix
Slice timing fix
2020-03-25
Tweak to RMANOVA covariate - names figure titles with covariate info
2020-03-24
Slicetiming - made manual settings first priority, then BIDS, then DICOM
Slicetiming - made option for Siemens thingies
2020-03-21
Fixed Display results SPM option
Slicetiming - Adjusted for Siemens 7T being in ms, comapred with 3T being in seconds.
2020-03-19
Added option to save slicetiming settings (https://osabrainresearch.atlassian.net/wiki/x/KAB_Jg )
2020-03-03
Fixed a SUIT 2nd level stats error
2020-02-29
Might have fixed another hi-res fMRI bug
2020-02-27
Might have fixed hi-res fMRI bug
2020-02-25
Possible bug fix for SUIT vector model
Fixed fMRI timetrend with VERBOSE on bug
2020-02-06
fmri VOI new measure - fixed bug
2020-02-03
fmri VOI timetrends - fixed bug that appeared 3 weeks ago
2020-01-24
fmritype - now show ID in listÂ
2020-01-21
Covariates - dealing with covariates with spaces and dashes
Set stats - re-load covariates when looking at a set
2020-01-20
Preprocessing and set stats - fixed to bugs due to recent changesÂ
2020-01-18
Several changes to stats GUI to fix 2nd level analysis problem. Tidying of code to improve reliability in the future.
Display/mean - corrected an SPM file (spm_orthviews.m) that sometimes causes problemsÂ
2020-01-17
Basic stats - allowed for empty top-left cell (A1), and corrected error where sometimes would miscount rowsÂ
2020-01-16
Basic stats - fixed error
2019-11-14
SUIT fMRI boxcar - fixed bug (is it also there in whole-brain?)
SUIT fMRI - Added an error checking for corrupted files when doing 1st-level fMRI analysis (and prior step, smoothing, if VERBOSE is on)
2019-12-13
Project configuration - fix bugs with adding groups and new studies (subjects), and deleting studies (errors in recent release of MATGLAB - 2019b and 2018b at least)
Adjusted display results GUI
2019-12-09
fixed bug - drifter would not make a unique folder - now has "n" in name
Changed slice timing "a" in folder to be towards end, not start
Created a help option if run
>> cspm_paramastr_fmri2019-12-05
fMRI: slice-timing option now works as long as have BIDS format; install MRIcroGL. Probably won't work yet with Philips (as Paul)
Fixed timetrend make difference bug
2019-12-05
fMRI preprocess boxcar bug fix
Create new set - no longer default set-folder to project folder
2019-12-04
Large number of changes
Display functional - option to skip CorelDraw/pdf creation
Fixed Plot Combined bug
Added individual vector for physiology (new fmritype)
2019-11-19
Correlation tool tweaks
2019-11-14
Tweaked VOI-VOI connectivity GUi to maybe work with MATLAB 2018a...
Added an error checking for corrupted files when doing fMRI analysis
2019-11-13
Correlation tool and VOI-VOI connectivity tidied....VOI still slow
2019-11-12
More tweaks to correlation tool, including option to create image of correlation matrix (in future will be used for VOI connectivity)
2019-11-08
Improved Correlation tool
2019-10-30
fMRI VOI-to-VOI connectivity: can do lots of VOI.... (up to 81 VOI / ~3200 combinations)
2019-10-23
fMRI VOI-to-VOI connectivity: Adds more output tables in Excel file
2019-10-23
New fMRI VOI-to-VOI connectivity
2019-10-16
VOI extract values now checks for NaN's
VOI correlation measures and VOI-connectivity (from Stats GUI) working better than before...
Link to common folder for sharing files:
2019-10-14
Fixed 3D visualization bug wrt saving lighting
Tweaks to ASL, analysis GUI's
2019-09-04
SPM updated (lots of files)
2019-09-03
3D viz: Added button to create surface
CSPM - added menu item to do the same
SUIT: bug fixes on added option to mask whole-brain fMRI images with SUIT VOIÂ
Small cosmetic tweaks to 3D GUI, some analysis files
2019-08-31 (fixed bugs 2019-09-02)
SUIT: added option to mask whole-brain fMRI images with SUIT VOI before running suit-reslice
2019-08-20
SUIT: summaries for fMRI, VBM etc. now use SUIT template, and set the image center to be in the cerebellum
2019-08-15
Working on vector option: made corrections, should work with SUIT (but still being tested)
Tweaked Projects GUI
2019-08-14
Added a feature in fmri type settings to view the convolved version of the vector (which is what is included as regressor values in the 1st-level SPM model).
2019-08-13
More work on vector common - found a problem that is fixed.
2019-08-09
Fixed vector common preprocessing step (not fully tested)
2019-07-30
Fixed vector common option in fmritype setup