restructure for manuscipt

greydongilmore · Dec 10, 2020 · 70540fb · 70540fb
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diff --git a/Figures/Old/AFLE colormap.tif b/Figures/Old/AFLE colormap.tif
diff --git a/Figures/Old/AFLE.psd b/Figures/Old/AFLE.psd
diff --git a/Figures/Old/AFRE colormap.tif b/Figures/Old/AFRE colormap.tif
diff --git a/Figures/Old/AFRE.psd b/Figures/Old/AFRE.psd
diff --git a/Figures/Old/AFRE_fMRIprep_colormap.tif b/Figures/Old/AFRE_fMRIprep_colormap.tif
diff --git a/Figures/Old/Distance/PW_dist_Diff.tif b/Figures/Old/Distance/PW_dist_Diff.tif
diff --git a/Figures/Old/Distance/PW_dist_Oas.tif b/Figures/Old/Distance/PW_dist_Oas.tif
diff --git a/Figures/Old/Distance/PW_dist_PD.tif b/Figures/Old/Distance/PW_dist_PD.tif
diff --git a/Figures/Old/Distance/PW_dist_Sig.tif b/Figures/Old/Distance/PW_dist_Sig.tif
diff --git a/Figures/Old/Distance/Sig distances.xlsx b/Figures/Old/Distance/Sig distances.xlsx
diff --git a/Figures/Old/Error calc.xlsx b/Figures/Old/Error calc.xlsx
diff --git a/README.md b/README.md
@@ -1,20 +1,34 @@
-# afids clinical
+# AFIDs Clinical
+
+## Introduction
 
 * Linear transforms of fcsv to MNI are at: [/input/input_linear_transform](/input/input_linear_transform)
 * Non-linear transforms of fcsv to MNI are at: [/input/input_mniTransform_fmriprep](/input/input_mniTransform_fmriprep)
 
-## FIDS to check
+### Repository structure
+
+The repository has the following scheme:
+```
+├── README.md
+├── data
+|   ├── fid_standards
+|   ├── input_fid_MNI_linear
+|   ├── input_fid_MNI_nonlinear
+|   ├── input_fid_native
+|   ├── OASIS-1
+|   └── demographics.tsv
+├── manuscript
+|   └── final_figures
+├── results
+|   ├── avg_fcsv
+|   └── plots
+└── src
+    ├── matlab
+    └── python
+```
 
-## Subject(s) to ignore?
+## Analysis
 
-- sub-172
-- sub-184 (hydrocephalus)
-- sub-192 (previous electrode)
+## Manuscript files
 
-## Subjects not completed by raters
 
-| raters    | subjects not done |
-|:----------|:------------------|
-| Alaa      | 126, 151, 152, 179, 220   |
-| Maggie    | 116, 118, 124, 126, 127, 130, 134, 143, 152, 220  |
-| Greydon   | 116,118,124,126,127,130,134,143,151,152,179,195,196,220   |
diff --git a/analysis/Old/scratch_analysis.xlsx b/analysis/Old/scratch_analysis.xlsx
diff --git a/input/OASIS-1/OAS1_0010_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0010_MR1_T1_MEAN.fcsv b/input/OASIS-1/OAS1_0010_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0010_MR1_T1_MEAN.fcsv
diff --git a/input/OASIS-1/OAS1_0086_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0086_MR1_T1_MEAN.fcsv b/input/OASIS-1/OAS1_0086_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0086_MR1_T1_MEAN.fcsv
diff --git a/input/OASIS-1/OAS1_0101_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0101_MR1_T1_MEAN.fcsv b/input/OASIS-1/OAS1_0101_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0101_MR1_T1_MEAN.fcsv
diff --git a/input/OASIS-1/OAS1_0109_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0109_MR1_T1_MEAN.fcsv b/input/OASIS-1/OAS1_0109_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0109_MR1_T1_MEAN.fcsv
diff --git a/input/OASIS-1/OAS1_0114_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0114_MR1_T1_MEAN.fcsv b/input/OASIS-1/OAS1_0114_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0114_MR1_T1_MEAN.fcsv
diff --git a/input/OASIS-1/OAS1_0117_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0117_MR1_T1_MEAN.fcsv b/input/OASIS-1/OAS1_0117_MR1_T1_MEAN.fcsv → data/OASIS-1/OAS1_0117_MR1_T1_MEAN.fcsv
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diff --git a/input/demographics.tsv → data/demographics.tsv b/input/demographics.tsv → data/demographics.tsv
diff --git a/input/MNI152NLin2009bAsym_MEAN_postQC.fcsv → ...ards/MNI152NLin2009bAsym_MEAN_postQC.fcsv b/input/MNI152NLin2009bAsym_MEAN_postQC.fcsv → ...ards/MNI152NLin2009bAsym_MEAN_postQC.fcsv
diff --git a/input/mni_jon_standard/mni_jon_standard.mat → ...rds/mni_jon_standard/mni_jon_standard.mat b/input/mni_jon_standard/mni_jon_standard.mat → ...rds/mni_jon_standard/mni_jon_standard.mat
diff --git a/..._jon_standard/sub-MNI2009cAsym_afids.fcsv → ..._jon_standard/sub-MNI2009cAsym_afids.fcsv b/..._jon_standard/sub-MNI2009cAsym_afids.fcsv → ..._jon_standard/sub-MNI2009cAsym_afids.fcsv
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diff --git a/...3_FID32_T1w_AT_201803030_mnifmriprep.fcsv → ...3_FID32_T1w_AT_201803030_mnifmriprep.fcsv b/...3_FID32_T1w_AT_201803030_mnifmriprep.fcsv → ...3_FID32_T1w_AT_201803030_mnifmriprep.fcsv
diff --git a/...6_FID32_T1w_AT_201803015_mnifmriprep.fcsv → ...6_FID32_T1w_AT_201803015_mnifmriprep.fcsv b/...6_FID32_T1w_AT_201803015_mnifmriprep.fcsv → ...6_FID32_T1w_AT_201803015_mnifmriprep.fcsv
diff --git a/...7_FID32_T1w_AT_201803021_mnifmriprep.fcsv → ...7_FID32_T1w_AT_201803021_mnifmriprep.fcsv b/...7_FID32_T1w_AT_201803021_mnifmriprep.fcsv → ...7_FID32_T1w_AT_201803021_mnifmriprep.fcsv
diff --git a/...8_FID32_T1w_AT_201803015_mnifmriprep.fcsv → ...8_FID32_T1w_AT_201803015_mnifmriprep.fcsv b/...8_FID32_T1w_AT_201803015_mnifmriprep.fcsv → ...8_FID32_T1w_AT_201803015_mnifmriprep.fcsv
diff --git a/...1_FID32_T1w_AT_201803013_mnifmriprep.fcsv → ...1_FID32_T1w_AT_201803013_mnifmriprep.fcsv b/...1_FID32_T1w_AT_201803013_mnifmriprep.fcsv → ...1_FID32_T1w_AT_201803013_mnifmriprep.fcsv
diff --git a/...2_FID32_T1w_AT_201803014_mnifmriprep.fcsv → ...2_FID32_T1w_AT_201803014_mnifmriprep.fcsv b/...2_FID32_T1w_AT_201803014_mnifmriprep.fcsv → ...2_FID32_T1w_AT_201803014_mnifmriprep.fcsv
diff --git a/...3_FID32_T1w_AT_201803013_mnifmriprep.fcsv → ...3_FID32_T1w_AT_201803013_mnifmriprep.fcsv b/...3_FID32_T1w_AT_201803013_mnifmriprep.fcsv → ...3_FID32_T1w_AT_201803013_mnifmriprep.fcsv
diff --git a/...8_FID32_T1w_AT_201803013_mnifmriprep.fcsv → ...8_FID32_T1w_AT_201803013_mnifmriprep.fcsv b/...8_FID32_T1w_AT_201803013_mnifmriprep.fcsv → ...8_FID32_T1w_AT_201803013_mnifmriprep.fcsv
diff --git a/...87_FID32_T1w_GG_20190725_mnifmriprep.fcsv → ...87_FID32_T1w_GG_20190725_mnifmriprep.fcsv b/...87_FID32_T1w_GG_20190725_mnifmriprep.fcsv → ...87_FID32_T1w_GG_20190725_mnifmriprep.fcsv
diff --git a/...93_FID32_T1w_GG_20190725_mnifmriprep.fcsv → ...93_FID32_T1w_GG_20190725_mnifmriprep.fcsv b/...93_FID32_T1w_GG_20190725_mnifmriprep.fcsv → ...93_FID32_T1w_GG_20190725_mnifmriprep.fcsv