updates 2017-08 August

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

2017-08-31

fMRI - fixed calculation of detrended and phys noise corrected mean files - was missing prefix in mean, and should have been labelled "mean..." since they are re-calculated.
Tweak to avoid some errors in subjects GUI.
Fix WHH load bug.

2017-08-27

Default 3D visualization to save images and movie
Fixed bug for file checking (only occurred with mask calculation errors)
Mean/mask calculation - added another check for problems with files.

2017-08-26

Tidied FIR visualization, and 3D GUI.

2017-08-25

Added some error checking in mean calculation.

2017-08-24

Display more information when copying rsfMRI files during setup.

2017-08-23

Fixed drifter bug.

2017-08-18

Change to not crash with CorelDraw problems while creating pdf files for group summaries.

2017-08-17

Set preprocess color....
SUIT - offers to copy T1 VOI to other modality VOI's
Set DRIFTER to resp 8:26, periodics 1/1
fMRI LMRP revived .... last used on SPM5!

2017-08-16

fMRI FIR 1st level - checks for errors and gives some messages with guidance depending on what problem is found.
Fix load error - occurred when a covariate had a space in the name ("MSNA ")
Adjusted subject export to allow for more than 10 groups (currently limited to ~50, can increase if needed).
Check for CorelDraw problems in creating overlays (display results) - will give warning, but continue.
Show which project folders are missing

Display results - now comes up with set brain mask

View analyses - last 2-3 days, preprocessiing will have led to duplicate analyses. Re-run one preprocess to fix.
Stats GUI - will remember resize settings
CSPM GUI - changed setting to stop Noemi's illegal activity - will not remember clicks made during processing
fMRI rest - saves subject files with images (for loading into DPARFSA, for example)
FIR - 1st level designs, added error checking
Fixed day-old basic stats bug
Stats GUI fixed bug to do with folders

2017-08-15

Fixed ASL display results bug (last couple of days)
Tweaks to saving and retrieving old analyses (ones with different settings, for example)
DPARSFA - fixed subjects-read bug in later MATLAB (post 2013)

Technical note: DPARFSA.m line 464

% PMM - fix error of reads only one cell
IDCell = textscan(fid,'%s');
% IDCell = textscan(fid,'%s\n'); %YAN Chao-Gan. For compatiblity of MALLAB 2014b. IDCell = textscan(fid,'%s','\n');

DPARSF - Options to start GUI (and add path) in CSPM menu:

Sets: removed unused button, and added note about selecting multiple projects

Now show VOI folder in stats GUI

Added option in local settings to test CorelDraw settings

Fixed stats GUI load problem (last day only)
Analysis GUI - added set information on top-left, in separate panel (should be clearer!)

CSPM GUI now opens over spm's interactive GUI, below menu.

2017-08-14

Set view analyses: now shows all saved analyses, not just recently run
fMRI slice timing - fixed mean calculation
fMRI preprocessing - more information displayed
fMRI preprocessing - if error during mean calculation, tries again (slice timing step)
Study folders - more information
Set analyze GUI - filter now not case sensitive.
Fixed bug after filtering to no results

2017-08-13

Some FIR visualization working - 3D, overlays, glass brain.

Get to this from View analyes:

Tidying some fMRI bugs introduced the last few days

2017-08-11

Individual subject: show folders

Tweaked study data Browse (subjects GUI) to be slightly clearer
Rename con files in subfolders - Emily's special

Bug fixes: basic stats, working with repeated fmritypes in same study.

2017-08-10

Bug fixes in fMRI preprocessing - fix various programming errors introduced in the last couple of days.
Added slice timing correction option (Analysis GUI) - will ONLY work for non-interleaved axila bottom-to-top aquisitions!!!
Option to create a design matrix for the - this is useful for creating FIRST design matrices. To get the values, double-click on the Design image in the SPM window; this copies the design matrix to the command window, where you can copy the values by selecting them or using the temporary variable "ans"

Set analyses: can go straight to SPM Results

VOI timetrend: plots in a figure (like global timetrend)

Fixed overlay mask-blobs error
DRIFTER: may need to use harmonics of 1 and 1, not 3 and 4 - checking today.

2017-08-09

Added "DRIFTER" physiologic noise correction option (info)

Tidied fMRI options in analysis GUI (above)
Tided 2nd level stats GUI
Fixed a few bugs introduced over the past couple of days
Adjusted DRIFTER to allow for initial slice to be empty.
SUIT VOI - looks for old fMRI with different name (works for Sophie)
Tidying FIR, still not ready for 2nd level

2017-08-08

Bug fixing for last few days....
Tidied 2nd level stas GUI to remove GM scaling
Fixed view stats bug (last day)
2nd level - link to help page on global scaling options.
SUIT - yes to all option for copying VOI added. * All modalities
SUIT - tidied some messages, if manual is not selected will use T1 VOI for other modalities
Records resting state measures
Mean images: if CorelDraw is not installed or not working, the preprocessing will not repeat calculating mean images etc.
Project info: added some formatting

2017-08-07

View analyses fixed; GUi tweaked.
Bug with Kasia's fMRI processing: tweaked an spm file to reduce chance of error (spm_data_read.m). This file had a repeated error at one processing step, but when the process was tried a couple of times it worked ok, This is odd because the same file had the error for several iterations, but just interrupting the routine then trying again fixed the error.
Project file info: From project setup GUI, clicking the "Project Info (Studies and Files)" will open an Excel file with links to folders

SUIT fMRI: fixed summary images - was incorrectly using whole brain instead of SUIT images.
CSPM menu: Apply T1 DARTEL normalization to other files

fMRI - fixed "REST' mislabelling from 2 days ago.

2017-08-06

*** one file missing, will update tonight - this will not work today *** Viewing results: from stats GUI, now can click "View analyses" to get a list

Select an analysis and click "Open GUI.." to open in the usual "Display Results" GUI.

FIR: tidied up group analyses - still no way of visuaalizing, but each delta is analyzed with group analysis.

2017-08-05

FIR: tweaking visualization - overlays have option to move colorbars to separate figure.
rsfMRI: resting state series should be marked as fmritype "none" and the problem will skip the first level, and copy the files to the set folder so these can more easily be used by other rsfMRI software

2017-08-04

FIR: use brainmasklots (normalized version) for masking blobs, and the normalized brainmask (unsmoothed) for creating the surface.
Brain mask: crude/liberal brainmask fix with a morphological operation (https://osabrainresearch.atlassian.net/wiki/x/ZoAKBQ); this mask is used for maskng SPM analyses in fMRI, etc.

Display motion from selected fMRI series - from Visualize study GUI:

Set analysis GUI - Added filter options, and highlighted description field

FIR for single subject - added brainmask when calculating blobs.

2017-08-03

Mean calculations - gives message if there is an SPM warning (happens if a study's T1 image is off)
Project GUI - fixed spelling mistake that was bothering Zeynab, did more tidying
fMRI RFx: added some error messages and suggestions for 1st level analyses

2017-08-02

Projects GUI - tidied up, including making Copy/Convert option more obvious since that is the usual way data should be moved into the project

SUIT: ASL, DTI and T2 note will use specific masks (not tested yet!)
Fix single-subject set bug whereby summary calculations would fail (specifically ALL/ANY masks)
fMRI - give a few more messages (detrend) showing where files are located, and prefix of input/output files
SUIT: fMRI, will look for series-specific mask

2017-08-01

Analysis GUI: default to no T1 rotations, remembers T1 rotation setting and never overwrite setting