test data folder -> test_data

petmri · Apr 22, 2024 · 57f242a · 57f242a
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diff --git a/test data/BBB data p19/Dynamic_t1w.nii → test_data/BBB data p19/Dynamic_t1w.nii b/test data/BBB data p19/Dynamic_t1w.nii → test_data/BBB data p19/Dynamic_t1w.nii
diff --git a/test data/BBB data p19/fa10.nii → test_data/BBB data p19/fa10.nii b/test data/BBB data p19/fa10.nii → test_data/BBB data p19/fa10.nii
diff --git a/test data/BBB data p19/fa2.nii → test_data/BBB data p19/fa2.nii b/test data/BBB data p19/fa2.nii → test_data/BBB data p19/fa2.nii
diff --git a/test data/BBB data p19/fa5.nii → test_data/BBB data p19/fa5.nii b/test data/BBB data p19/fa5.nii → test_data/BBB data p19/fa5.nii
diff --git a/test data/BBB data p19/header dynamic.txt → test_data/BBB data p19/header dynamic.txt b/test data/BBB data p19/header dynamic.txt → test_data/BBB data p19/header dynamic.txt
diff --git a/test data/BBB data p19/header fa10.txt → test_data/BBB data p19/header fa10.txt b/test data/BBB data p19/header fa10.txt → test_data/BBB data p19/header fa10.txt
diff --git a/test data/BBB data p19/header fa2.txt → test_data/BBB data p19/header fa2.txt b/test data/BBB data p19/header fa2.txt → test_data/BBB data p19/header fa2.txt
diff --git a/test data/BBB data p19/header fa5.txt → test_data/BBB data p19/header fa5.txt b/test data/BBB data p19/header fa5.txt → test_data/BBB data p19/header fa5.txt
diff --git a/...p19/processed/Rsquared_t1_fa_fit_fa10.nii → ...p19/processed/Rsquared_t1_fa_fit_fa10.nii b/...p19/processed/Rsquared_t1_fa_fit_fa10.nii → ...p19/processed/Rsquared_t1_fa_fit_fa10.nii
diff --git a/...ata/BBB data p19/processed/T1_AIF_roi.nii → ...ata/BBB data p19/processed/T1_AIF_roi.nii b/...ata/BBB data p19/processed/T1_AIF_roi.nii → ...ata/BBB data p19/processed/T1_AIF_roi.nii
diff --git a/...a/BBB data p19/processed/T1_brain_roi.nii → ...a/BBB data p19/processed/T1_brain_roi.nii b/...a/BBB data p19/processed/T1_brain_roi.nii → ...a/BBB data p19/processed/T1_brain_roi.nii
diff --git a/...a p19/processed/T1_map_t1_fa_fit_fa10.nii → ...a p19/processed/T1_map_t1_fa_fit_fa10.nii b/...a p19/processed/T1_map_t1_fa_fit_fa10.nii → ...a p19/processed/T1_map_t1_fa_fit_fa10.nii
diff --git a/...a/BBB data p19/processed/T1_noise_roi.nii → ...a/BBB data p19/processed/T1_noise_roi.nii b/...a/BBB data p19/processed/T1_noise_roi.nii → ...a/BBB data p19/processed/T1_noise_roi.nii
diff --git a/...BB data p19/processed/User Inputs Log.txt → ...BB data p19/processed/User Inputs Log.txt b/...BB data p19/processed/User Inputs Log.txt → ...BB data p19/processed/User Inputs Log.txt
diff --git a/test data/BBB data p19/processed/gm.roi → test_data/BBB data p19/processed/gm.roi b/test data/BBB data p19/processed/gm.roi → test_data/BBB data p19/processed/gm.roi
diff --git a/...ocessed/results/Dyn-1_2cxm_fit_Ktrans.nii → ...ocessed/results/Dyn-1_2cxm_fit_Ktrans.nii b/...ocessed/results/Dyn-1_2cxm_fit_Ktrans.nii → ...ocessed/results/Dyn-1_2cxm_fit_Ktrans.nii
diff --git a/...results/Dyn-1_2cxm_fit_ktrans_ci_high.nii → ...results/Dyn-1_2cxm_fit_ktrans_ci_high.nii b/...results/Dyn-1_2cxm_fit_ktrans_ci_high.nii → ...results/Dyn-1_2cxm_fit_ktrans_ci_high.nii
diff --git a/.../results/Dyn-1_2cxm_fit_ktrans_ci_low.nii → .../results/Dyn-1_2cxm_fit_ktrans_ci_low.nii b/.../results/Dyn-1_2cxm_fit_ktrans_ci_low.nii → .../results/Dyn-1_2cxm_fit_ktrans_ci_low.nii
diff --git a/...sed/results/Dyn-1_ex_tofts_fit_Ktrans.nii → ...sed/results/Dyn-1_ex_tofts_fit_Ktrans.nii b/...sed/results/Dyn-1_ex_tofts_fit_Ktrans.nii → ...sed/results/Dyn-1_ex_tofts_fit_Ktrans.nii
diff --git a/...lts/Dyn-1_ex_tofts_fit_ktrans_ci_high.nii → ...lts/Dyn-1_ex_tofts_fit_ktrans_ci_high.nii b/...lts/Dyn-1_ex_tofts_fit_ktrans_ci_high.nii → ...lts/Dyn-1_ex_tofts_fit_ktrans_ci_high.nii
diff --git a/...ults/Dyn-1_ex_tofts_fit_ktrans_ci_low.nii → ...ults/Dyn-1_ex_tofts_fit_ktrans_ci_low.nii b/...ults/Dyn-1_ex_tofts_fit_ktrans_ci_low.nii → ...ults/Dyn-1_ex_tofts_fit_ktrans_ci_low.nii
diff --git a/...essed/results/Dyn-1_patlak_fit_Ktrans.nii → ...essed/results/Dyn-1_patlak_fit_Ktrans.nii b/...essed/results/Dyn-1_patlak_fit_Ktrans.nii → ...essed/results/Dyn-1_patlak_fit_Ktrans.nii
diff --git a/...sults/Dyn-1_patlak_fit_ktrans_ci_high.nii → ...sults/Dyn-1_patlak_fit_ktrans_ci_high.nii b/...sults/Dyn-1_patlak_fit_ktrans_ci_high.nii → ...sults/Dyn-1_patlak_fit_ktrans_ci_high.nii
diff --git a/...esults/Dyn-1_patlak_fit_ktrans_ci_low.nii → ...esults/Dyn-1_patlak_fit_ktrans_ci_low.nii b/...esults/Dyn-1_patlak_fit_ktrans_ci_low.nii → ...esults/Dyn-1_patlak_fit_ktrans_ci_low.nii
diff --git a/...ocessed/results/Dyn-1_patlak_fit_rois.xls → ...ocessed/results/Dyn-1_patlak_fit_rois.xls b/...ocessed/results/Dyn-1_patlak_fit_rois.xls → ...ocessed/results/Dyn-1_patlak_fit_rois.xls
diff --git a/...cessed/results/Dyn-1_tofts_fit_Ktrans.nii → ...cessed/results/Dyn-1_tofts_fit_Ktrans.nii b/...cessed/results/Dyn-1_tofts_fit_Ktrans.nii → ...cessed/results/Dyn-1_tofts_fit_Ktrans.nii
diff --git a/...esults/Dyn-1_tofts_fit_ktrans_ci_high.nii → ...esults/Dyn-1_tofts_fit_ktrans_ci_high.nii b/...esults/Dyn-1_tofts_fit_ktrans_ci_high.nii → ...esults/Dyn-1_tofts_fit_ktrans_ci_high.nii
diff --git a/...results/Dyn-1_tofts_fit_ktrans_ci_low.nii → ...results/Dyn-1_tofts_fit_ktrans_ci_low.nii b/...results/Dyn-1_tofts_fit_ktrans_ci_low.nii → ...results/Dyn-1_tofts_fit_ktrans_ci_low.nii
diff --git a/test data/BBB data p19/processed/wm.roi → test_data/BBB data p19/processed/wm.roi b/test data/BBB data p19/processed/wm.roi → test_data/BBB data p19/processed/wm.roi
diff --git a/test data/BBB data p19/processed/wm2.roi → test_data/BBB data p19/processed/wm2.roi b/test data/BBB data p19/processed/wm2.roi → test_data/BBB data p19/processed/wm2.roi
diff --git a/...sub-01/ses-01/A_DCE_mc_bfc_normR1info.mat → ...sub-01/ses-01/A_DCE_mc_bfc_normR1info.mat b/...sub-01/ses-01/A_DCE_mc_bfc_normR1info.mat → ...sub-01/ses-01/A_DCE_mc_bfc_normR1info.mat
diff --git a/...ses-01/B_DCE_mc_bfc_normfitted_R1info.mat → ...ses-01/B_DCE_mc_bfc_normfitted_R1info.mat b/...ses-01/B_DCE_mc_bfc_normfitted_R1info.mat → ...ses-01/B_DCE_mc_bfc_normfitted_R1info.mat
diff --git a/...-01/ses-01/DCE_mc_bfc_normAIF_fitting.fig → ...-01/ses-01/DCE_mc_bfc_normAIF_fitting.fig b/...-01/ses-01/DCE_mc_bfc_normAIF_fitting.fig → ...-01/ses-01/DCE_mc_bfc_normAIF_fitting.fig
diff --git a/...b-01/ses-01/DCE_mc_bfc_norm_image_ROI.fig → ...b-01/ses-01/DCE_mc_bfc_norm_image_ROI.fig b/...b-01/ses-01/DCE_mc_bfc_norm_image_ROI.fig → ...b-01/ses-01/DCE_mc_bfc_norm_image_ROI.fig
diff --git a/...-01/ses-01/DCE_mc_bfc_norm_timecurves.fig → ...-01/ses-01/DCE_mc_bfc_norm_timecurves.fig b/...-01/ses-01/DCE_mc_bfc_norm_timecurves.fig → ...-01/ses-01/DCE_mc_bfc_norm_timecurves.fig
diff --git a/...ub-01/ses-01/DCE_mc_bfc_normdynamicCt.nii → ...ub-01/ses-01/DCE_mc_bfc_normdynamicCt.nii b/...ub-01/ses-01/DCE_mc_bfc_normdynamicCt.nii → ...ub-01/ses-01/DCE_mc_bfc_normdynamicCt.nii
diff --git a/...DS_test/derivatives/sub-01/ses-01/VFA.nii → ...DS_test/derivatives/sub-01/ses-01/VFA.nii b/...DS_test/derivatives/sub-01/ses-01/VFA.nii → ...DS_test/derivatives/sub-01/ses-01/VFA.nii
diff --git a/...b-01/ses-01/anat/T1_map_t1_fa_fit_sub-01_ses-01_space-DCEref_desc-bfczunified_VFA.nii.txt b/...b-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!
+  <a href="matlab:helpPopup MException" style="font-weight:bold">MException</a> 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!
+  <a href="matlab:helpPopup MException" style="font-weight:bold">MException</a> 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!
+  <a href="matlab:helpPopup MException" style="font-weight:bold">MException</a> 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 <a href="matlab:matlab.internal.language.introspective.errorDocCallback('parse_preference_file')" style="font-weight:bold">parse_preference_file</a>
+File not found: /script_preferences.txt
+
+Error in <a href="matlab:matlab.internal.language.introspective.errorDocCallback('T1mapping_fit', '/home/mrispec/code/ROCKETSHIP/parametric_scripts/custom_scripts/T1mapping_fit.m', 37)" style="font-weight:bold">T1mapping_fit</a> (<a href="matlab: opentoline('/home/mrispec/code/ROCKETSHIP/parametric_scripts/custom_scripts/T1mapping_fit.m',37,0)">line 37</a>)
+    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 <a href="matlab:matlab.internal.language.introspective.errorDocCallback('parse_preference_file')" style="font-weight:bold">parse_preference_file</a>
+File not found: script_preferences.txt
+
+Error in <a href="matlab:matlab.internal.language.introspective.errorDocCallback('T1mapping_fit', '/home/mrispec/code/ROCKETSHIP/parametric_scripts/custom_scripts/T1mapping_fit.m', 37)" style="font-weight:bold">T1mapping_fit</a> (<a href="matlab: opentoline('/home/mrispec/code/ROCKETSHIP/parametric_scripts/custom_scripts/T1mapping_fit.m',37,0)">line 37</a>)
+    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!
+  <a href="matlab:helpPopup MException" style="font-weight:bold">MException</a> with properties:
+
+    identifier: 'MATLAB:getReshapeDims:notRealInt'
+       message: 'Size arguments must be real integers.'
+         cause: {}
+         stack: [2×1 struct]
+    Correction: []
+
+addpath
+{Error using <a href="matlab:matlab.internal.language.introspective.errorDocCallback('addpath')" style="font-weight:bold">addpath</a>
+Not enough input arguments.
+} 
+help addpath
+ <strong>addpath</strong> Add folder to search path.
+    <strong>addpath</strong> 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.
+
+    <strong>addpath</strong> FOLDERNAME1 FOLDERNAME2 FOLDERNAME3 ...  prepends all the 
+    specified folders to the path.
+
+    <strong>addpath</strong> ... -END    appends the specified folders.
+    <strong>addpath</strong> ... -BEGIN  prepends the specified folders.
+    <strong>addpath</strong> ... -FROZEN disables folder change detection for folders
+                        being added.
+
+    Use the functional form of <strong>addpath</strong>, such as 
+    <strong>addpath</strong>('folder1','folder2',...), when the folder specification is 
+    a variable or string.
+
+    P = <strong>addpath</strong>(...) 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 <a href="matlab:help rmpath -displayBanner">rmpath</a>, <a href="matlab:help pathtool -displayBanner">pathtool</a>, <a href="matlab:help path -displayBanner">path</a>, <a href="matlab:help savepath -displayBanner">savepath</a>, <a href="matlab:help userpath -displayBanner">userpath</a>, <a href="matlab:help genpath -displayBanner">genpath</a>, <a href="matlab:help rehash -displayBanner">rehash</a>.
+
+    <a href="matlab:doc addpath">Documentation for addpath</a>
+
diff --git a/...01/ses-01/anat/sub-01_ses-01_T1map.nii.gz → ...01/ses-01/anat/sub-01_ses-01_T1map.nii.gz b/...01/ses-01/anat/sub-01_ses-01_T1map.nii.gz → ...01/ses-01/anat/sub-01_ses-01_T1map.nii.gz
diff --git a/..._space-DCEref_desc-bfczunified_VFA.nii.gz → ..._space-DCEref_desc-bfczunified_VFA.nii.gz b/..._space-DCEref_desc-bfczunified_VFA.nii.gz → ..._space-DCEref_desc-bfczunified_VFA.nii.gz
diff --git a/...es-01_space-DCEref_desc-brain_mask.nii.gz → ...es-01_space-DCEref_desc-brain_mask.nii.gz b/...es-01_space-DCEref_desc-brain_mask.nii.gz → ...es-01_space-DCEref_desc-brain_mask.nii.gz
diff --git a/...1/dce/sub-01_ses-01_desc-AIF_T1map.nii.gz → ...1/dce/sub-01_ses-01_desc-AIF_T1map.nii.gz b/...1/dce/sub-01_ses-01_desc-AIF_T1map.nii.gz → ...1/dce/sub-01_ses-01_desc-AIF_T1map.nii.gz
diff --git a/...01/dce/sub-01_ses-01_desc-bfcz_DCE.nii.gz → ...01/dce/sub-01_ses-01_desc-bfcz_DCE.nii.gz b/...01/dce/sub-01_ses-01_desc-bfcz_DCE.nii.gz → ...01/dce/sub-01_ses-01_desc-bfcz_DCE.nii.gz
diff --git a/...ta/sub-01/ses-01/sub-01_ses-01_T1w.nii.gz → ...ta/sub-01/ses-01/sub-01_ses-01_T1w.nii.gz b/...ta/sub-01/ses-01/sub-01_ses-01_T1w.nii.gz → ...ta/sub-01/ses-01/sub-01_ses-01_T1w.nii.gz