Updates 2022

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.

  Open

  

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”)

  Open

  

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

• LMGS

  • The processing is now volume-by-volume, if there is enough memory to load the entire fMRI series; otherwise it remains slice-by-slice (much slower)

    • In addition be being faster, volume-by-volume may reduce write errors

  • 4D files are properly supported

• fMRI speeding up smoothing and DRIFTER with local processing option; this copies files to a temporary local folder to avoid writing over the network; potential 3 x or more speed-up, and may be more reliable

• Never overwrite button more obvious

• Set edit folder and add comments work from Preprocess GUI (comments work in Sets GUI)

• Sets - split large project(s) into smaller sets; this may be useful to spread preprocessing (e.g., CAT). Example below shows HCP split into ~11 sets of 1000 each

• 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.

>> P = spm_select(1,'image');

>> flags.vox_above_th = 0.5;

>> 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)