From 0d6044801b53a83a909215d2ea1878bd2542269f Mon Sep 17 00:00:00 2001
From: Emily Kubota <emily.kubota@gmail.com>
Date: Wed, 24 Aug 2022 10:59:45 -0700
Subject: [PATCH] made tensor2fa more flexible

---
 utilities/AFQ_mrtrix_tensor2metric.m | 73 ++++++++++++++++++++++++++++
 1 file changed, 73 insertions(+)
 create mode 100644 utilities/AFQ_mrtrix_tensor2metric.m

diff --git a/utilities/AFQ_mrtrix_tensor2metric.m b/utilities/AFQ_mrtrix_tensor2metric.m
new file mode 100644
index 0000000..e971316
--- /dev/null
+++ b/utilities/AFQ_mrtrix_tensor2metric.m
@@ -0,0 +1,73 @@
+function [status, results] = AFQ_mrtrix_tensor2metric(in_file, out_file, ...
+                                         mask_file, metric, verbose,mrtrixVersion)
+
+%
+% Calculate diffusion tensors.
+%
+% Parameters
+% ----------
+% in_file: The name of a dti file in .mif format
+% out_file: The name of the resulting fa file in .mif format
+% mask_file: The name of a mask file in .mif format (default to the entire
+%             volume). 
+% metric: metric to compute options are 'md', 'fa', 'ad', 'rd'
+% note: only will work with mrTrix3
+% 
+% Returns
+% -------
+% status: whether (0) or not (non-zero) the operation succeeded
+% results: the results of the operation in stdout
+%
+% Notes
+% -----
+% http://www.brain.org.au/software/mrtrix/tractography/preprocess.html
+%
+% Edited GLU 06.2016:
+%        1.- Remove absolute paths
+%        2.- Include mrTrix version
+% 
+% Edited ECK & XY 08.2022: 
+%       1. only include functionality for mrTrix3
+%       2. make more flexible for multiple metrics
+
+if mrtrixVersion ~=3 
+    error('mrTrix version must be 3.')
+end 
+
+if notDefined('verbose')
+    verbose = true;
+end
+
+if notDefined('bkgrnd')
+    bkgrnd = false;
+end
+
+func1Name = 'tensor2metric';
+func1NameOpt = '-fa';
+func2Name = 'mrcalc';
+func2NameOpt = '-mult';
+
+switch metric
+    case 'fa'
+        func1NameOpt = '-fa';
+    case 'md'
+        func1NameOpt = '-adc';
+    case 'ad'
+        func1NameOpt = '-ad';
+    case 'rd'
+        func1NameOpt = '-rd';
+end
+
+% If no mask file was provided, calculate this over the entire volume
+if notDefined('mask_file')
+    cmd_str = sprintf('%s %s %s %s', func1Name,    in_file, ... 
+                                  func1NameOpt, out_file);
+% Otherwise, use the mask file provided: 
+else
+    cmd_str = sprintf('%s %s %s - | %s - %s %s %s', ...
+                       func1Name, in_file, func1NameOpt, ...
+                       func2Name, mask_file, func2NameOpt, out_file);
+end
+
+% Send it to mrtrix:
+[status,results] = AFQ_mrtrix_cmd(cmd_str, bkgrnd, verbose,mrtrixVersion);
\ No newline at end of file