These release notes refer to the latest CSPM changes, which are uploaded to Google Drive (help getting files). Sometimes files outside of the CSPM folder are updated; if so, the notes will mention “matlab update”, in which case select the “matlab” profile option in the sync software; otherwise, just use the “CSPM” profile in the sync software.
MATLAB version: 2023a (as of April 2023, there may be problems with earlier versions). Recommend 2024a.
ANTS - fixed problem with Jacobian, adjusted GM segmentation to allow finer structures
Basic stats - does not write residuals (slow for large studies)
Preclinical ANTs documentation https://osabrainresearch.atlassian.net/wiki/x/BYCemw
Preclinical - ANTs runs through VBM pipeline for DBM and GM modulated
Preclinical - Several ANTs bug fixes….
Preclinical - Fixed a bug on registration
Preclinical - Added brain extraction; added more steps (10:41 pm LA time)
Preclinical- Added ANTs test processing button. Needs WSL, Ubuntu, conda and ants installed (ANTs )
Preclinical- will show messages if error in anatomical unified processing
fMRI SUIT - added file/folder info and clearer error message for file problems with SUIT reslice/normalize to template
Analysis GUI - fMRI, can now enter protocol ID to select (saves scrolling through 1000+…)
fMRI - If there is an error in the normalize (whole brain and SUIT), the preprocessing will stop. Previously, it tried to continue (and led to errors at summary stage). This will make if easier to see where the errors are occuring.
Projects - fixed error for first-time running in new install
Physiology - added IMT, some tweaks
Preclinical - shows template voxel size
fMRI, places where mean is calculated: in case of error, added check to detect corrupted images; if found, information will be shown.
Slice overlay - refreshed file so that update should replace existing slice_overlay.m files (and let “Overlays” work - for Noemi!)
Preclinical - (2nd update, 6:25 pm LA) Fixed scaling (in native space, now scales up when smoothing); fixed possible DTI bug
Preclinical - Does DTI, VBM slightly better organized
CSPM - fewer warnings when creating pdf’s.
Minor updates - reviewing fMRI, since there are errors at times. But these are often file corruption issues, not software bugs
Analysis - Faster GUI loading with large number of protocols
Minor - fMRI new measure, note to say work off unsmoothed images; SUIT preprocess hide long message.
Physiology - lots of changes.
Sets - new GUI to more easily edit sets, adding and removing studies, and creating groups.
fMRI motion - at set level
Cat12 - updated; should re-run CAT processing (ideally); option to redo CAT12 processing
Analysis GUI: fixed error whereby previous settings were sometimes not saved (might get one or two new errors that pop up, should be easily fixed)
Analysis GUI - can skip warning about different numebrs of files/series
Physiology - resampling option for exporting physiology files
CSPM GUI - Set Stats, option to not load previous (saves time for large sets)
fMRI distortion correction - leaves 3D files2024-03-07
SNR - adjusted to work better with outliers
T2 info - works on subfolders, little bit of tidying
preclinical - fixed bug
preclinical - fixed bug
VOI values - tweaked, bug fix
VOI values - now have option to get spectra
Sets GUI - scrolls to selected set on startup
DTI info GUI - preprocessing should run on subfolders (not tested yet)
fMRI - lmrp and intensity normalization now no longer force 32-bit real (hopefully leave at int16)
fMRI - distortion correction: Will set up on local folder (see doc)
CAT12 - updated
3D to 4D - use the code from cat12, 50 x faster!
fMRI - distortion correction, will loop through fmritypes
fMRI - distortion correction, fixed the replication of existing protocols; default to no distortion correction
fMRI - distortion correction option - see https://osabrainresearch.atlassian.net/wiki/x/BYA2fw
NOTE: All fmri protocols will be re-done, since there is no option set in existing protocols.
