updates 2018-07-23 to 2019-05

Owned by Paul Macey (admin)
Last updated: Jul 31, 2019
4 min read

These release notes refer to the latest CSPM changes, which are uploaded to Google Drive.

2019-05-24
  • Fix DRIFTER error that would sometimes occur with non-integer TR values.
  • Fix file checking tool (only runs where there are errors)
2019-05-16
  • Fixing bugs with sub-mm resolution in voxel size and smoothing for whole-brain and SUIT.
2019-05-08
  • Changes to allow for sub-mm resolution in voxel size and smoothing for whole-brain and SUIT.
2019-05-01
  • Fixed another SUIT fMRI bug - 1st level for RFx (due to recent voxel size option).
2019-04-29
  • Fixed SUIT fMRI bug (due to recent voxel size option).
2019-04-23
  • Avoid errors with recent MATLAB releases (2019a, 2018b) in subjects GUI (incorporated mew 'findjobj" file).
2019-04-16
  • Updated VOI cross section - uses volumes toolbox, reports X/Y/Z mm, includes quantitative extraction
2019-04-04
  • Possible fix to Set load error (Noemi).
2019-03-26
  • Updated the VOI cross-sectional area (under CSPM VOI menu)

2019-03-25
  • Fixed type-change to work for float32 to int16 (and others).
2019-02-13
  • Reslice will now ask about interpolation
  • Supersample of T1 uses sinc 7 interpolation
2019-02-08
  • Found and fixed the bug introduced a few days earlier.
2019-02-04
  • Tweak to possible fix an error T1 preprocessing
2019-01-31
  • DTI: tweak to possible fix an error with calculating mean b0 (Noemi)
2019-01-30
  • DTI: adjusted for HCP data (b0 are actually b-value = 5, not 0)
  • Supersampling: fixed bug with single value for voxel size.
2019-01-29
  • Supersampling is now set up: define in local settings, and it will create files during T1 preprocessing.
2018-12-14
  • Fixed FIR bug that would occur with fMRI protocols with two or more repeats.
  • Included some code for creating brain pictures from FreeSurfer (needs to be manually turned on, contact Paul).
2018-10-26
  • Tweaked SUIT preprocessing so that spectra will run.
2018-19-19
  • SUIT fMRI - connectivity fix, should work (not tested yet).
  • Excel files - does not create links to some files that don't exist.
2018-09-25
  • Fixed MRS voxel mask bug.
2018-09-18
  • SUIT VBM - fixed saved name; showed up incorrectly in stats GUI (had whole-brain smoothing; actual images not affected, they use the correct SUIT smoothing).
2018-09-13
  • Allow resting state VOI to have spectra.
2018-09-09
  • Tweaked resting state
  • Added beta of MRS voxel
  • Check for Siemens "mini-file" in some T1 series - delete from rawimages.
2018-08-15
  • Cleaned excess messages for T1 combine (only when > 1 T1's).
2018-08-13
  • Updated Diffusion toolbox
2018-08-10
  • New fMRI - still some issues with resting state series
  • Multi-modality - works with existing sets (preprocessed before 2018-08)
  • FSL-compatible VOI - adjusted to remove spaces from filename, since FSL will give an error.
  • Tweaked CSPM GUI
  • Working on conn toolbox setup, not ready yet but some files changed.
2018-08-09
  • Added feature to create correlation map from VOI timetrend (connectivity).
  • Fixed bug in VOI timetrend.
2018-08-08
  • Fine tuning correlations, getting filenames that describe contents; better screen messages.
  • VOI timetrend (fMRI menu) now allows for multiple VOI's to be selected (to make Emily happy).
  • Fixed bedpost bug with copying files.
2018-08-07
  • Several bug fixes; still working on VOI GUIs (multi-modality, new fMRI measures).
  • Fixed database load bug introduced yesterday (only ocurred with empty groups).
  • Multi-modality correlations between measures working
  • Added descriptive stats to multi-modality; tidied figure axis labels when have underscore.
  • Repaired "View Analyses" on stats GUI
  • FSL bedpost now changes permissions when copying locally, so works in lab.
  • Tidied project and local settings GUIS
2018-08-06
  • ...and like wise (from below) in Sets project loading: 
  • To make Kasia and Noemi happy, they can now filter the studies for the copy/convert step:

  • Fixed FSL/bedpost to have DTI files FSL-compatible (no nifti rotations), and brian mask in correct space.
  • Bedpost will now by default copy files locally to Linux VM and run from there (in folder /working/fsl/[study]/DTI...). Option to change in settings

  • Correlations - now running on VOI; have option to leave open
  • Correlations save files
  • Have descriptive stats as part of correlations
  • Tidied "fMRI" and "ASL" modalities that should not be there for analysis in preprocessing
  • Quite a few underlying changes, so there could be the odd error introduced. This is in preparation for later features.  
2018-08-03
  • Updates: Correlations now work - might be some tweaks later, but basic functionality is there. Access either with button or menu:

  • Correlations 1st pass working; need to fix rows/columns
  • Working on multi-modality, not complete yet
2018-07-31
  • Correlations not currently working
  • GUI tweak for bedpost
  • Bedpost tweak - tried parallel processing, does not work
2018-07-30
  • Basic voi correlations running (Excel file output)
  • Added bedpost (FSL probability fiber tracking) in preprocessing options
  • VOI multimodality - GUI allows selection of measure, correlations by measure working in beta mode
  • Added preprocessing lines
2018-07-28
  • Altered preprocessing to work with multi-modality
  • Some more work on multi-modality
  • Display during preprocessing - added lines
  • Add link to this page on CSPM GUI

2018-07-27
  • Fixed DTI run one subject
2018-07-26
  • Fixed basic stats bug that happened with changing threshold
  • Fixed ASL preprocessing bug - may have only occurred with combined fMRI and ASL
  • Tidied CSPM GUI
  • Added option to delete spm_*.pdf files created by SPM

2018-07-23
  • Tidied project deletion; added note to project GUI (does not yet do physiology or metrics)