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change runner cmd, remove wildcard from run_dce_auto since it can be …
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…used in preference file
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lsaca05 committed Apr 29, 2024
1 parent fe41766 commit 8771f4e
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Showing 2 changed files with 7 additions and 7 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/run_DCE.yml
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ 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/; cd('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.gz')

- name: Run DCE
uses: matlab-actions/run-command@v2
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12 changes: 6 additions & 6 deletions run_dce_auto.m
Original file line number Diff line number Diff line change
Expand Up @@ -32,24 +32,24 @@ function run_dce_auto(subject_tp_path, subject_source_path)
tmp = dir(strcat(subject_tp_path, script_prefs.dynamic_files));
dynamic_files = cellstr(strcat(tmp.folder, '/', tmp.name));

tmp = dir(strcat(subject_tp_path, script_prefs.aif_files, '*'));
tmp = dir(strcat(subject_tp_path, script_prefs.aif_files));
aif_files = cellstr(strcat(tmp.folder, '/', tmp.name));

tmp = dir(strcat(subject_tp_path, script_prefs.roi_files, '*'));
tmp = dir(strcat(subject_tp_path, script_prefs.roi_files));
roi_files = cellstr(strcat(tmp.folder, '/', tmp.name));

tmp = dir(strcat(subject_tp_path, script_prefs.t1map_files, '*'));
t1map_files = cellstr(strcat(tmp(1).folder, '/', tmp(1).name));
tmp = dir(strcat(subject_tp_path, script_prefs.t1map_files));
t1map_files = cellstr(strcat(tmp.folder, '/', tmp.name));

if ~strcmp(script_prefs.noise_files,'')
tmp = dir(strcat(subject_tp_path, script_prefs.dynamic_files, '*'));
tmp = dir(strcat(subject_tp_path, script_prefs.dynamic_files));
noise_files = cellstr(strcat(tmp.folder, '/', tmp.name));
else
noise_files = '';
end

if ~strcmp(script_prefs.drift_files,'')
tmp = dir(strcat(subject_tp_path, script_prefs.dynamic_files, '*'));
tmp = dir(strcat(subject_tp_path, script_prefs.dynamic_files));
drift_files = cellstr(strcat(tmp.folder, '/', tmp.name));
else
drift_files = '';
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