Updates 2021

Owned by Paul Macey
Jan 25, 2022
5 min read

old updates

2021-12-29

  • Tidied Subjects GUI

    • Study actions are only available when a study is selected (to avoid “Select study first” warning)

    • Autofit columns now works properly; click button or press “A“ key (case does not matter); keypress works when figure is selected

    • Labels and tooltip info text are clarified & corrected

 

2021-12-09

  • Added filter for fMRI

2021-12-02

  • Fixed analysis bug with GUI…. may be there with other GUI’s

  • Updates to CAT12

2021-12-01

  • Fixed add new subject

2021-11-23

  • Fix - Set Load and analyze sound bring up new GUI

2021-11-18

  • Lots of changes to GUI’s, as part of updating to matlab’s uifigures.

  • DICOM convert: fixed bug in specifying code

  • Updated cat 12

  • Started adding CAT 12 to analysis - not finished yet!!

2021-10-14

  • Multiple sets: now have option to merge groups of same name

https://osabrainresearch.atlassian.net/wiki/x/AQDcW

 

2021-10-13

  • Updated REST

  • Can now select 2 or more sets to load (in Sets GUI)

  • Some tweaks to stats apps, should not alter existing functions

2021-09-09

  • T2 maps - from Bruker files - bleeding edge

 

2021-09-07

  • Sets: fixed blank study names

2021-08-27

  • Rodent DTI:

  • Place DTI nifti files in a folder (can be single *.nii.gz file); can leave out b0 file (this appears to be included in the 4D nii.gz file)

  • Start GUI

     

  • Go through 8 steps

     

2021-08-26

  • CSPM local settings: fixed local settings error - did not work remotely because a quirk of file naming with migration to new GUIs

    • To run local settings after stating CSPM, either go to Options menu, or on command line type >> cspm_local 

2021-08-12

  • Project copy and coreg - deal with multiple physiology

  • Set analysis -fix bug

  • Survey - download qualtrics SR 

2021-08-09

  • Bruker DTI: DICOM convert should work - include "method" file with DICOM files 

  • Test with DTI, run one

2021-08-05

  • 64 to 32: can select multiple

2021-08-02

  • cspm stats set load - possible fix for error when loading

2021-07-08

  • physiology - viewing and peak detection tidied

  • tools - app to create paced breathing videos

2021-06-11

  • db connection: added more information if connection fails (from local settings)

2021-06-03

  • fMRI slice timing: if BIDS does not have slice timing info, will check DICOM (instead of crashing)

  • Programming changes to help with conversion utility for CCHS 2004 data

2021-05-29

  • VOI values - option to have multiple VOI (in folder), and save Excel files in output folder

2021-05-04

  • Fixed bug with fMRI show-results option

2021-04-28

  • Fixed rare bug with SUIT measures not showing in Stats GUI

2021-04-19

  • Tweaks for R2021a compatibility

2021-04-15

  • Sydney: put in workaround for database table that disappeared ("subject_covariate"); it is essentially unused in Sydney.

    • Only use number covariates; "metrics" are the better way to most variables anyway.

2021-04-14

  • Sydney: older versions of MATLAB will cause error when starting CSPM due to GUI ("App") incompatibility

    • Use startup file in Z:\Sys Admin\MATLAB

    • In MATLAB, find the location of your startup file with

    • >> which startup

    • Replace this with the one from the share drive

    • If CSPM fails on startup, this new file will file will delete the "App" and try again with the old GUI

  • Updated some missing files on the cloud

2021-04-12

  • Added help for installing python Bruker to nifti conversion. In short, 1) install python according to the instructions, 2) install the bruker2nifti in python (easy), then 3) find the python gui file.

2021-03-31

  • CSPM: resize options now move windows based on edge of MATLAB window

2021-03-26

  • General: migration of back code to work with MATLAB 2021a (database connections especially)

  • CSPM: converted to MATLAB "App" (needed to maintain compatibility with future MATLAB releases)

2021-03-25

  • fmri type: 1) add vector common error fixed; Delete counts and shows number of fMRI studies with type; if more than one, a second confirmation is required (because it'll screw up those project fMRI studies)

2021-03-18

  • Stats GUI - fmri list font not as small

2021-03-16

  • Extract data from VOI: now has a GUI, but just does one VOI at a time

  • Can do all individual voxels in VOI 

2021-03-09
2021-03-01

  • Exporting from "Display orthviews with multiple views" updated with latest export_fig, and MATLAB 2020b tweaks.

    • Also checks for ghostview, which is a free program that needs to be installed for the export to work

  • Physiology: peak detection for rate calculation now functional at a minimal level: can detect and edit peaks, save rate, re-edit peaks.

  • PPI - now will try to reload new measure into Stats GUI. There are also two options to force reload, on in the main GUI (top circle) and one that will be enabled after the PPI has run (lower circle).

2021-02-16

  • Tweaks to NBS - fix bug, history saves in NBS folder

2021-02-13

  • NBS help page started

  • fMRI VOIxVOI connectivity saves correlation values etc. in format that NBS can read

  • Added Network-Based Statistics (NBS) toolbox (subfolder of CSPM)

  • CSPM buttons to start: NBS starts GUI, Man opens manual, Clear removes history so NBS wqill open the the demo example data (useful for tutorial in manual).

2021-02-11

  • Fixed database bug when subject id (number only) has 6 or more digits

  • Removed floating "loading" message for fMRI VOI-to-VOI

  • VOI r-maps (new measure of fMRI connectivity wrt VOI seed): made fix that may help when there are -ve values

CSPM forces the r-maps to "int16" format, which lets us see negative values.

Can check the file type of old problem files, and see whether it's "uint16" for example, which does not allow negative values. The old code just picked the file type based on the fMRI files, which may well have been unit16. The "u" stands for unsigned, which means positive only.