ReadMe for archive

There are several .zip folders in this archive. The contents of each .zip folder will be explained below. 

**Note the numbering in Table 1 (in the paper) is different than the data numbering in this archive.  
Data #	Table 1 #	
3	1	
6	2	
5	3	
1	4	
4	5	
7	6	
8	7	
		
9	8	
11	9	
10	10	
12	11	

Code and Stats.zip 
	▪	Final Stats 
	▪	AllDataforSAS_2021_best_final.xlsx: this excel file has all of the data which is imputed into the statistical code. The colums of the data are labeled. “Subject” refers to the Data#. Image ID indicates the data type (sarcomere length, “S”; fascicle length, “F”; muscle volume “V”) followed by the image number. For example, “S20” means that it is the 20th sarcomere length image for which data was taken. “Side” indicates left or right arm. “Stroke” is either Y if the participant had a stroke or N is they did not have a stroke. For those who are Y for “Stroke” the “Paretic” column is Y if this arm is their paretic arm and N if this arm is their non-paretic arm. For non-stroke participants the column “Non-dominant” will have a Y if this is their non-dominant arm and a N if it it their dominant arm. “Length” is the data point (mean sarcomere length for that image, single fascicle length within an image, muscle volume for that biceps brachia). Other columns are as follows: “FM” - Fugel-Meyer Assessment, “TSS” - Time since stroke, “Gender”, “Age”. 
	▪	FINAL_SAScode_04152021.sas: This is the SAS code for running the GLMMs and the statistical analysis for the muscle volume in this study. The code takes in the data from AllDataforSAS_2021_best_final.xlsx. 
	▪	FINAL_SAScode_04152021-results.pdf: this is the final output of the SAS code which is used to describe the stats in the paper. 
	▪	Parameters_for_SHG_Processing.xlsx: This excel file indicates the parameters which are inputted to the codes (PickSarcomereFramesandMeasureLengths_aa_05022018.m and Sarcomere_LowEMG.m) for processing the second harmonic generation (SHS) images.
	▪	PickSarcomereFramesandMeasureLengths_aa_05022018.m: This is the code for processing the SHG images and should be run in the folder with the raw .dat file and .txt file (with the identical root names) (see SHG_stroke.zip and SHG_nonstroke.zip). The point of this code is to select images with sarcomeres and export a mean sarcomere length for each selected image.
	▪	Sarcomere_LowEMG.m: this code takes the output from the PickSarcomereFramesandMeasureLengths_aa_05022018.m and determines which image frames occurred when the EMG was below 3 SD above the mean baseline EMG. The EMG (.mat) and .xlsx inputs for this code can be found in the (SHG_stroke.zip and SHG_nonstroke.zip)

US_Images.zip 
	▪	This zip folder contains the 3 raw images per arm, per individual. The images are labeled with data#_arm_image#. The data # and image # correspond to the fascicle length measures inputed into AllDataforSAS_2021_best_final.xlsx.

Segmentations_from_MRI.zip 
	▪	Biceps
	▪	This folder contains the segmented biceps muscle (both long and short head) in a .obj file. The .obj files are labeled data#_arm.
	▪	Humerus	
	▪	This folder contains the segmented humerus in a .obj file. The .obj files are labeled data#_arm. Some individuals had humeri which were not captured within the entire upper arm MRI. For these individuals there is a .obj file labeled upper and lower, which refers to a proximal set image collection and a distal image collection, respectively. 
	▪	MRI Segmentation.xlsx: this file has two sheets. The humerus sheet has the values for humerus length and the muscle volume sheet has the values for contractile volume (volume muscle - fat), total volume, %fat, and fat only volume. 

SHG_Non-Stroke.zip & SHG_Stroke.zip 
	▪	Each folder is labeled with the data#. Each folder has a left and right folder with the following:
	⁃	.dat and .txt : these are the raw SHG data and its associated txt file. These files are needed to run the PickSarcomereFramesandMeasureLengths_aa_05022018.m code. 
	⁃	[.dat folder name]_noavg_SarcomereMeasurements.xlsx file is the output of the PickSarcomereFramesandMeasureLengths_aa_05022018.m code
	⁃	SarcomereData_CodeOutput_EMGnoFilt.xlsx is the output of the Sarcomere_LowEMG.m. 
	⁃	.mat : there are .mat files for the trial EMG and the baseline EMG