diff --git a/test data/BBB data p19/Dynamic_t1w.nii b/test_data/BBB data p19/Dynamic_t1w.nii similarity index 100% rename from test data/BBB data p19/Dynamic_t1w.nii rename to test_data/BBB data p19/Dynamic_t1w.nii diff --git a/test data/BBB data p19/fa10.nii b/test_data/BBB data p19/fa10.nii similarity index 100% rename from test data/BBB data p19/fa10.nii rename to test_data/BBB data p19/fa10.nii diff --git a/test data/BBB data p19/fa2.nii b/test_data/BBB data p19/fa2.nii similarity index 100% rename from test data/BBB data p19/fa2.nii rename to test_data/BBB data p19/fa2.nii diff --git a/test data/BBB data p19/fa5.nii b/test_data/BBB data p19/fa5.nii similarity index 100% rename from test data/BBB data p19/fa5.nii rename to test_data/BBB data p19/fa5.nii diff --git a/test data/BBB data p19/header dynamic.txt b/test_data/BBB data p19/header dynamic.txt similarity index 100% rename from test data/BBB data p19/header dynamic.txt rename to test_data/BBB data p19/header dynamic.txt diff 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data/BIDS_test/derivatives/sub-01/ses-01/B_DCE_mc_bfc_normfitted_R1info.mat b/test_data/BIDS_test/derivatives/sub-01/ses-01/B_DCE_mc_bfc_normfitted_R1info.mat similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/B_DCE_mc_bfc_normfitted_R1info.mat rename to test_data/BIDS_test/derivatives/sub-01/ses-01/B_DCE_mc_bfc_normfitted_R1info.mat diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_normAIF_fitting.fig b/test_data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_normAIF_fitting.fig similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_normAIF_fitting.fig rename to test_data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_normAIF_fitting.fig diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_norm_image_ROI.fig b/test_data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_norm_image_ROI.fig similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_norm_image_ROI.fig rename to test_data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_norm_image_ROI.fig diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_norm_timecurves.fig b/test_data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_norm_timecurves.fig similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_norm_timecurves.fig rename to test_data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_norm_timecurves.fig diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_normdynamicCt.nii b/test_data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_normdynamicCt.nii similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_normdynamicCt.nii rename to test_data/BIDS_test/derivatives/sub-01/ses-01/DCE_mc_bfc_normdynamicCt.nii diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/VFA.nii b/test_data/BIDS_test/derivatives/sub-01/ses-01/VFA.nii similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/VFA.nii rename to test_data/BIDS_test/derivatives/sub-01/ses-01/VFA.nii diff --git a/test_data/BIDS_test/derivatives/sub-01/ses-01/anat/T1_map_t1_fa_fit_sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.txt b/test_data/BIDS_test/derivatives/sub-01/ses-01/anat/T1_map_t1_fa_fit_sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.txt new file mode 100644 index 0000000..d41151a --- /dev/null +++ b/test_data/BIDS_test/derivatives/sub-01/ses-01/anat/T1_map_t1_fa_fit_sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.txt @@ -0,0 +1,245 @@ +Starting execution at April 22, 2024 12:27:43 +User selected files: +../../test data/BIDS_test/derivatives/sub-01/ses-01/anat//sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.gz +User selected TE/TR/FA/TI: + 2 + 5 + 10 + 12 + 15 + +User selected fit: +t1_fa_fit +User selected CPUs: + 4 + +User selected Neuroecon: + 0 + +User selected email: +User selected data order: +xyzn +User selected output basename: +T1_map +User selected only odd echoes: + 0 + +User selected smooth size (Gaussian standard deviation): + 0 + +User selected fit all voxels: + 1 + +User selected ROIs: +User selected tr: +8 +User selected r^2 threshold: + 0.6000 + +Gpufit detected. GPU will be utilized for T1 mapping. +T1 mapping failed! Sad! + MException with properties: + + identifier: 'MATLAB:getReshapeDims:notRealInt' + message: 'Size arguments must be real integers.' + cause: {} + stack: [2×1 struct] + Correction: [] + +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') +Starting execution at April 22, 2024 12:27:57 +User selected files: +../../test data/BIDS_test/derivatives/sub-01/ses-01/anat//sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.gz +User selected TE/TR/FA/TI: + 2 + 5 + 10 + 12 + 15 + +User selected fit: +t1_fa_fit +User selected CPUs: + 4 + +User selected Neuroecon: + 0 + +User selected email: +User selected data order: +xyzn +User selected output basename: +T1_map +User selected only odd echoes: + 0 + +User selected smooth size (Gaussian standard deviation): + 0 + +User selected fit all voxels: + 1 + +User selected ROIs: +User selected tr: +8 +User selected r^2 threshold: + 0.6000 + +Gpufit detected. GPU will be utilized for T1 mapping. +T1 mapping failed! Sad! + MException with properties: + + identifier: 'MATLAB:getReshapeDims:notRealInt' + message: 'Size arguments must be real integers.' + cause: {} + stack: [2×1 struct] + Correction: [] + +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') +Starting execution at April 22, 2024 12:27:59 +User selected files: +../../test data/BIDS_test/derivatives/sub-01/ses-01/anat//sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.gz +User selected TE/TR/FA/TI: + 2 + 5 + 10 + 12 + 15 + +User selected fit: +t1_fa_fit +User selected CPUs: + 4 + +User selected Neuroecon: + 0 + +User selected email: +User selected data order: +xyzn +User selected output basename: +T1_map +User selected only odd echoes: + 0 + +User selected smooth size (Gaussian standard deviation): + 0 + +User selected fit all voxels: + 1 + +User selected ROIs: +User selected tr: +8 +User selected r^2 threshold: + 0.6000 + +Gpufit detected. GPU will be utilized for T1 mapping. +T1 mapping failed! Sad! + MException with properties: + + identifier: 'MATLAB:getReshapeDims:notRealInt' + message: 'Size arguments must be real integers.' + cause: {} + stack: [2×1 struct] + Correction: [] + +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') +{Error using parse_preference_file +File not found: /script_preferences.txt + +Error in T1mapping_fit (line 37) + script_prefs = parse_preference_file(preferencePath, 0, ... +} +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') +{Error using parse_preference_file +File not found: script_preferences.txt + +Error in T1mapping_fit (line 37) + script_prefs = parse_preference_file(preferencePath, 0, ... +} +addpath('/home/mrispec/code/ROCKETSHIP') +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') +Starting execution at April 22, 2024 12:38:58 +User selected files: +../../test data/BIDS_test/derivatives/sub-01/ses-01/anat//sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.gz +User selected TE/TR/FA/TI: + 2 + 5 + 10 + 12 + 15 + +User selected fit: +t1_fa_fit +User selected CPUs: + 4 + +User selected Neuroecon: + 0 + +User selected email: +User selected data order: +xyzn +User selected output basename: +T1_map +User selected only odd echoes: + 0 + +User selected smooth size (Gaussian standard deviation): + 0 + +User selected fit all voxels: + 1 + +User selected ROIs: +User selected tr: +8 +User selected r^2 threshold: + 0.6000 + +Gpufit detected. GPU will be utilized for T1 mapping. +T1 mapping failed! Sad! + MException with properties: + + identifier: 'MATLAB:getReshapeDims:notRealInt' + message: 'Size arguments must be real integers.' + cause: {} + stack: [2×1 struct] + Correction: [] + +addpath +{Error using addpath +Not enough input arguments. +} +help addpath + addpath Add folder to search path. + addpath FOLDERNAME prepends the specified folder to the current + matlabpath. Surround FOLDERNAME in quotes if the name contains a + space. If FOLDERNAME is a set of multiple folders separated by path + separators, then each of the specified folders will be added. + + addpath FOLDERNAME1 FOLDERNAME2 FOLDERNAME3 ... prepends all the + specified folders to the path. + + addpath ... -END appends the specified folders. + addpath ... -BEGIN prepends the specified folders. + addpath ... -FROZEN disables folder change detection for folders + being added. + + Use the functional form of addpath, such as + addpath('folder1','folder2',...), when the folder specification is + a variable or string. + + P = addpath(...) returns the path prior to adding the specified paths. + + Examples + addpath c:\matlab\work + addpath /home/user/matlab + addpath /home/user/matlab:/home/user/matlab/test: + addpath /home/user/matlab /home/user/matlab/test + + See also rmpath, pathtool, path, savepath, userpath, genpath, rehash. + + Documentation for addpath + diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_T1map.nii.gz b/test_data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_T1map.nii.gz similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_T1map.nii.gz rename to test_data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_T1map.nii.gz diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.gz b/test_data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.gz similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.gz rename to test_data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.gz diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_space-DCEref_desc-brain_mask.nii.gz b/test_data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_space-DCEref_desc-brain_mask.nii.gz similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_space-DCEref_desc-brain_mask.nii.gz rename to test_data/BIDS_test/derivatives/sub-01/ses-01/anat/sub-01_ses-01_space-DCEref_desc-brain_mask.nii.gz diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/dce/sub-01_ses-01_desc-AIF_T1map.nii.gz b/test_data/BIDS_test/derivatives/sub-01/ses-01/dce/sub-01_ses-01_desc-AIF_T1map.nii.gz similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/dce/sub-01_ses-01_desc-AIF_T1map.nii.gz rename to test_data/BIDS_test/derivatives/sub-01/ses-01/dce/sub-01_ses-01_desc-AIF_T1map.nii.gz diff --git a/test data/BIDS_test/derivatives/sub-01/ses-01/dce/sub-01_ses-01_desc-bfcz_DCE.nii.gz b/test_data/BIDS_test/derivatives/sub-01/ses-01/dce/sub-01_ses-01_desc-bfcz_DCE.nii.gz similarity index 100% rename from test data/BIDS_test/derivatives/sub-01/ses-01/dce/sub-01_ses-01_desc-bfcz_DCE.nii.gz rename to test_data/BIDS_test/derivatives/sub-01/ses-01/dce/sub-01_ses-01_desc-bfcz_DCE.nii.gz diff --git a/test data/BIDS_test/rawdata/sub-01/ses-01/sub-01_ses-01_T1w.nii.gz b/test_data/BIDS_test/rawdata/sub-01/ses-01/sub-01_ses-01_T1w.nii.gz similarity index 100% rename from test data/BIDS_test/rawdata/sub-01/ses-01/sub-01_ses-01_T1w.nii.gz rename to test_data/BIDS_test/rawdata/sub-01/ses-01/sub-01_ses-01_T1w.nii.gz