fmri_grocer Grocer2.12

zshtom@stage.nitrcce.org (senhua zhu) — Wed, 27 Mar 2013 15:16:00 GMT

09/20/2011 fmri_grocer V1.0
* The first version of this toolbox release!
* This toolbox contains many kinds of kits that you may be interested in for fMRI data analysis.
* This toolbox is run and tested on SPM8 with MATLAB 7.6.0(R2008a) under the Linux.
* Most of the functions should be compatible with SPM5 and should also work smoothly under the Windows OS.

09/20/2011 fmri_grocer V1.1
* Optimize some output description of some functions
09/20/2011 fmri_grocer V1.2
* Update the manual
09/20/2011 fmri_grocer V1.3
* Fix two bugs of a function's output
09/21/2011 fmri_grocer V1.4
* Fix a bug in batch reslicing
09/21/2011 fmri_grocer V1.5
* Add two more functions in menu 7 (Avg imgs across same timepoints)
* Optimize some ouput description of some funcitons
09/28/2011 fmri_grocer V1.6
* Add one more functions to menu 6 & 7 separately; (Search & replace, View a 3d-variable)
* Optimize and improve some functions in menu 6.
09/30/2011 fmri_grocer V1.7
* Add ICC calculation to menu 3(CBF related batch...)
* Add CBF reconstruction function of one group of subjects to menu 3 (CBF calculation(SPM5/8 Only,Multi.Subjs))
* Improve the compatibility with REST toolbox itself
10/03/2011 fmri_grocer V1.8
* fix a bug in finding peak voxel function
10/05/2011 fmri_grocer V1.9
* Improve ICC algorithm in menu 3
* Add r-comparison function in menu 3
* Add one more function in menu7 (Yook displaying imgs as Mricro(n))
* Extend the menu8
* Restructure some functions of menu7 into menu8
* Add the funtion of restructuring your study files into what Grocer need (menu8)
* Fix two bugs in batch generating script
* Update Voxbo related functions (in house use only! If your linux system
also have installed Voxbo tools, then you can use this tool.)
10/05/2011 fmri_grocer V2.0
* Improve the funcion of Voxbo realted tools in menu 8
* Move the show histogram function from menu 3 to menu 4
10/08/2011 fmri_grocer V2.01
* Add 'Move each pair of hddr/img into separate folers' in menu 8.
This is useful especially when you want to put away your T1 imgs into separate folders
* Fix a bug in extracting the AAL/BA TCs when there is a different resolution between template and img
* Add a function of reslicing Multiple labeling image (e.g, AAL/BA template) in menu 7
* Add CBF reconstruction function that use different mask for different subj in menu 3
* Make the batch reslicing function to be compatible with .nii files
* Add check string in txt files to menu 6
* Enhance all the reslicing-related functions
* Make the CBF reconstruction functions be compatible with .nii images
10/17/2011 fmri_grocer V2.02
* Add 'Plot time course of txt/csv file' function to menu 8
* Improve the "View 3D variable" function in menu8
* Enhance 'show histogram' function in menu4
* Fix some bugs in several function in menu 3
* Add 'Bulid individual brain mask' function to menu7
* Add menu9
* Add "reorginaze files from full factorial design to flexiable design" to menu 8
* Enhance some function's flexiability
* Correct some spelling mistakes of file names
* Add ICC calculation for matrixes input to menu 3(CBF related batch...)
10/17/2011 fmri_grocer V2.03
* Add "Inquire AAL region names" function to menu4
* Remove 'ROI.mat 2 hdr/img in native space' from menu4
* Correct some indications of the pop out windows
* Optimize some functions
* Add "Rename all files under multiDirs' function to menu6
* Move "get time course" functions from menu3 to menu4
* Fix a bug in function "inquire voxel-space coord. in AAL" in menu5
* Display the exact version num in title of the toolbox
* Add 'switch red arrow on/off' function to menu 7
* Fix a bug in mean imgs calculation function in menu7
01/25/2012 fmri_grocer V2.04
* Add 'group files into folders' function in menu 8
* Add 'voxel-wise Pearson's r' function in menu3
* Add 'voxel-wise group variance' function in menu3
* Add existed file name checking into some related functions
* Improve the algorithm of some voxel-wise calculation
* Add "img 2 zscore (n-subjs)" function to menu3
* Intergrate all CBF calculation functions into one file in menu3
* Add "Switch crosshair ON/OFF" function to menu8
* Add existed file checking sub-function to many functions
* Add excellent "Create pipeline for standard preprocessing" function to menu1.
Use this function, you can finish all steps of preprocessing just with several clicks.
* Improve the flexibility of the folder/file selection in all functions of menu1 & 2,
and so does it to some other n-group-subject functions (including the CBF-reconstruction functions) in menu3.
After these updates, preprocessing becomes very easy.
01/25/2012 fmri_grocer V2.05
* Create a new menu "Image formate related..."
* Fix some bugs of the functions in previous version
* Add many subfunctions and separate many functions into sub-modules to make the main functions to be more flexible
* Add 'copy foder structure' function in menu 7
* Add 'list foders recursively' function in menu 7
* Add 'list file-related foders recursively' function in menu 7
* Add 'T1 segment' function in menu 1
* Optimize and enhance many functions's performance(e.g. rename functions...)
* Add Nifti-related tools to menu 6 ("Image formate related...")
* Add 'list out folders having specific folder size' function to menu 7
* Add 'move out folders having specific folder size' function to menu 7
* Improve the .nii & .img support of functions
* Update manual (quick start)
* Add "Enhenced Check-Reg" function to menu 8
* Add "Enlarge view of two Check-Reg Imgs" function to menu 8
* Add "Overlay SPM_T/F img by xjview" function to menu 8
* Add "4D -> 3D" & "3D -> 2D" etc. functions to menu 6
* Add "Implement (enhanced) standard preprocessing" function to menu 1, this
function is different from all other functions in menu1 as it will implement
what you specify directly after you finish all the selection
* Add some more testing functions about PCA-denosing into menu1 and menu9
02/22/2012 fmri_grocer V2.06
* Impressive update:
Intergrate the preprocessing and CBF calculation together in the
"Do (enhanced)-preprocessing & CBF Calc." function of menu1
with this function, you can run all preprocessing(including Slice-timing, Realign, Coregister,
Smooth, and Normalize) and potential CBF calculation for both of the BOLD and ASL-perfusion
data in a very flexiable way.
* Improve the method in acquiring individual masks for self-masked CBF calculation, which you can find the
Demo function in menu 8: Build individual mask with G. + W.
02/24/2012 fmri_grocer V2.07
* Improve the flexiability of the timecourse extracting function in menu 4
* Improve the algorithm of the individual mask in CBF calculation
* Add "hdr/img paire 2 Nii" function to menu6
* Improve (w)MeanCBF moving algorithm
* Enhance img-histogram showing function for mutiple masks
* Enhance "Do the (enhanced)-all preprocessing" function in menu1
* Add "Smooth self-masked imges" function in menu1
* Remove the REST-based subfunction in the two reslicing functions in menu8,
and just leave the one based on SPM
* improve the show imgage histogram function's output and flexiability
* Fix some bugs of some functions
* Add 'Make avi-movie of a sequence of images' function into menu9
* Improve the performance of some coordinate-related functions
* Improve the flexiblity of many functions in menu2
* Add 'Full factorial design (2nd level)' function into menu2
* Enhance and improve the flexibility of self-mask related functions
* Add 'Move specific subdirs up a level with parent folder name' function to menu7
* Improve performance of some file/folder related functions
* Improve performance of get timecourse and plot timecourse related functions
* Improve performance of statistic related functions in menu2
03/28/2012 fmri_grocer V2.08
* Improve performance of timecourse plotting function, and add a 'Plot time course(overlay)' to menu9
* Add 'Do PVE-correction for perfusion data' function for to menu3
* Add 'Do PVE-correction for perfusion data(n-group-subjs)' function for to menu3
* Improve the batch reslice function to make it can relice each img into a corresponding target space
* Update Get Timecourse functions to be compatible with individual space
* Reorginaze some functions into different menus to make the categories to be much clearer.
* Update the manual of Grocer. Brief description of the function was added for most of the functions list in Grocer.
04/03/2012 fmri_grocer V2.09
* Add "reslice imgs in original space function" into menu 8
* Switch menu 5/6 in the Grocer
* Fix a bug in implementing self-saved template file (*.m) in several functions (such as 'contrast all' function)
* Fix a file selectiong bug in 'Yoke displaying imgs as Mricro' function
* Fix a bug in the 'Full factorial design (2nd_level)' function
* Fix a bug in the 'BA/AAL multi. Labeling areas combination' function and improve its performance
* Add 'Linearly detrend' function to menu 9
* Add 'band pass filter' function to menu 9
* Add 'Manipulate selected paired-imgs(e.g. (i1-i2)./i1) ' function to menu 9
* Add 'Copy/Mov-out/Del-in filtered folders ' function to menu 7
* Improve the performance of 'Group files into folders(n-Subjs)' function
* Improve the performance of 'Do the (enhanced)-all preprocessing & CBF calculation' function
* Improve the performance of 'Full factorial design(2nd level)' function and fix a bug of this function
* Rename the enhanced Check-Reg function into 'Check-Reg up to 24 Imgs (paired-groups)', and improve the
flexibility of the checking fucniton.
* Add 'Del non-filtered files/folders of a dir' function to menu 7.
* Make the 4D->3D function be compatiable with .gz files
* Add functions of zip/unzip .gz files to menu 6
* Add Dicom conversion functions to menu 6
* Add functions of acquiring of SD-TC (corresponding to the TC acquiring functions) to menu 4
07/30/2012 fmri_grocer V2.10
* Fix a bug in the function of reconstructing foders for Grocer, in which it only recognized .img/hdr images.
* Fix a mistake in the function of generating script pipeline for preprocessing of BOLD data
* Fix a bug in the function of categorying 1st_level's con*.* images, and enhanc its performance.
* Use the old function of "filepart" to replace the new "filepart" in MATLAB2012 to make Grocer can be run under MATLAB 2012.
* Fix the problem of "The command line is too long" in importing Dicom images using dcm2nii command lines, and use dcm2nii function to replace SPM function in the function of menu 6
08/13/2012 fmri_grocer V2.11
* Add 'Overlay ROIs imgs on a Background img', 'Overlay three ROI imgs on a Background img' functions to menu 8
* The carton of the data organization in the manual updated.
* From this version, either of 'fmri_grocer', 'grocer' or 'fmrigrocer' can be used to start Grocer-toolbox in Matlab command window.
* Add 'Rename selected files to predifined names' function to menu 7
* Add 'value range selecting' function to functions of extracting time-courses.
* Enhance the 'value range selecting' function in the functions of extracting time-courses.
* Add 'Backconstruct folder structure from GROCER-needed ' function to menu 7
* Add 'Evaluate overlay between two groups of ROIs' function to menu 4
* Fix a bug in the function of listing files recursively
* Enhance the performance of in-house using 'Voxbo command' function in menu 9
* Spilt Voxbo related funtions into 3 parts in menu 9, and enhanced the performance of them separately
* Remove subfunction of "Move groups into specific subj folders" in menu9 which was run after using voxbo-tools
03/07/2013 fmri_grocer V2.12
* Enhance the 'Avg selected imgs across same timepoints' and 'Avg imgs across same timepoints (n-Group-Subj)' functions
* Fix a mistake in 'voxelwised ICC calculation' function
* Add "1st level design" function to the menu 2, which provides you to deal with 1st-level design in a batch way
* Fix a bug in "Group files into folders" function in the menu 7
* Add "Group selected-files into folders based on labeling" function in the menu 7
* Add "Import Dicom files with folder structure(SPM-based)" function in the menu 6
* Add "Granger Causal Connectivity Analysis" functions in the menu 9
* Enhance the "Run selected jobs" function in the main panel of Grocer.
* Add "Randomly split selected files/folders to two groups" function into menu 7
* Add "Calculate the Dice similarity coefficient" function into menu 9
* Add "Regress Tag-Ctrl from perfusion imgs' function into menu 3
* Add "Binarize the selected imgs(e.g. i1>0)(n-Group-Subj)' function into menu 9
* Add "Calculate the Dice similarity coefficient(two groups)" function into menu 9
03/19/2013 fmri_grocer V2.13
* Add "Flip images in original space" function into menu 8

fMRI Grocer Releases

fmri_grocer Grocer2.12