pref file path fix attempt, rename run_dce_auto->run_dce_cli, fix run…

…ner VFA input filename, add dce.json for test data
petmri · Apr 29, 2024 · 3fc05db · 3fc05db
1 parent 8771f4e
commit 3fc05db
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Showing 4 changed files with 15 additions and 6 deletions.
diff --git a/.github/workflows/run_DCE.yml b/.github/workflows/run_DCE.yml
@@ -36,12 +36,12 @@ jobs:
       - name: Run T1 mapping
         uses: matlab-actions/run-command@v2
         with:
-          command: addpath .; addpath dce/; addpath external_programs/; addpath external_programs/niftitools/; addpath parametric_scripts/; addpath parametric_scripts/custom_scripts/; T1mapping_fit('test_data/BIDS_test/rawdata/sub-01/ses-01/anat/', 'test_data/BIDS_test/derivatives/sub-01/ses-01/anat/', 'sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.gz')
+          command: addpath .; addpath dce/; addpath external_programs/; addpath external_programs/niftitools/; addpath parametric_scripts/; addpath parametric_scripts/custom_scripts/; T1mapping_fit('test_data/BIDS_test/rawdata/sub-01/ses-01/anat/', 'test_data/BIDS_test/derivatives/sub-01/ses-01/anat/', 'sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii')
 
       - name: Run DCE
         uses: matlab-actions/run-command@v2
         with:
-          command: run_dce_auto('test_data/BIDS_test/derivatives/sub-01/ses-01/')
+          command: run_dce_cli('test_data/BIDS_test/derivatives/sub-01/ses-01/')
 
       - name: Upload Ktrans result
         uses: actions/upload-artifact@v3

diff --git a/parametric_scripts/custom_scripts/T1mapping_fit.m b/parametric_scripts/custom_scripts/T1mapping_fit.m
@@ -1,7 +1,12 @@
 function T1mapping_fit(source_path, tp_path, file)
 % INPUTS
 %------------------------------------
-file_list = {strcat(tp_path, '/', file)};
+if (tp_path(end) ~= '/')
+    file_list = {strcat(tp_path, '/', file)};
+else
+    file_list = {strcat(tp_path, file)};
+end
+
 if ~(exist(file_list{1}, "file"))
     disp('VFA file missing!')
     disp(file_list)
@@ -28,7 +33,7 @@ function T1mapping_fit(source_path, tp_path, file)
 if isempty(json_list)
     % default FAs
     parameter_list = [2 5 10 12 15];
-    preferencePath = strcat('script_preferences.txt');
+    preferencePath = strcat('../../script_preferences.txt');
     script_prefs = parse_preference_file(preferencePath, 0, ...
         {'tr'});
     tr = script_prefs.tr;          % units ms, only used for T1 FA fitting

diff --git a/run_dce_auto.m → run_dce_cli.m b/run_dce_auto.m → run_dce_cli.m
@@ -1,9 +1,9 @@
-function run_dce_auto(subject_tp_path, subject_source_path)
+function run_dce_cli(subject_tp_path, subject_source_path)
     % Use full path to the subject timepoint as this function's argument.
     % Beware, try-catches are used to keep a batch script running.
 
     % Find and add subpaths 
-    mfilepath=fileparts(which('run_dce_auto'));
+    mfilepath=fileparts(which('run_dce_cli'));
     addpath(fullfile(mfilepath,'dce'));
     addpath(fullfile(mfilepath,'external_programs'));
     addpath(fullfile(mfilepath,'external_programs/niftitools'));

diff --git a/test_data/BIDS_test/rawdata/sub-01/ses-01/dce/sub-01_ses-01_DCE.json b/test_data/BIDS_test/rawdata/sub-01/ses-01/dce/sub-01_ses-01_DCE.json
@@ -0,0 +1,4 @@
+{
+    "RepetitionTime": 0.008012,
+    "FlipAngle": 15
+}