update project READMEs according to template [#27]

projects/autism_mri/README.md

@@ -1,25 +1,44 @@
-# query_6b2c09de69c29c29626f794757ea4c68
- 
+# autism_mri
+
 Repo to do LabelBuddy annotations of a corpus of Autism MRI literature
 
-## PubGet
-This process was initialized with a *pubget* call:
+## Papers
+
+### How the papers were obtained
+We ran the following bash command:
 
 ```bash
 pubget run -q "Brain Volume MRI 2022 Autism" pubget/test --labelbuddy --n_jobs 4
 ```
-
-The whole `pubget` output has been uploaded to OSF: https://osf.io/meya4
-
-## LabelBuddy
-We are currently annotating the following file:
-
-`projects/autism_mri/documents/documents_00001.jsonl`
-
-Which in the `pubget` output corresponds to:
-
-`query_6b2c09de69c29c29626f794757ea4c68/subset_allArticles_labelbuddyData/documents_00001.jsonl`
-
-And writing the annotation files found in:
-`projects/autism_mri/annotations/`
+### Where the full papers are stored
+The full pubget output is stored on OSF: [https://osf.io/meya4](https://osf.io/meya4).
+## Annotations
+### File(s) being annotated: 
+- `/projects/autism_mri/documents/documents_00001.jsonl`
+  - corresponding file in the pubget output: 
+    - `query_6b2c09de69c29c29626f794757ea4c68/subset_allArticles_labelbuddyData/documents_00001.jsonl`
+
+### Annotation labels:
+- FieldStrength: `<description of label1>`
+- Diagnosis: `<description of label2>` 
+- N_Total:
+- N_Total_Male:
+- N_Total_Female
+- N_Patients
+- N_Controls
+- N_Controls_Male
+- N_Controls_Female
+- N_Patients_Male
+- N_Patients_Female
+- Age_Mean
+- Age_Min
+- Age_Max
+- Scanner
+- AnalysisTool
+- MRI_Modality
+### Labels found in other projects as well:
+- `<label2>`
+
+### Instructions for annotators
+`<description>`
 

projects/cluster_inference/README.md

@@ -0,0 +1,50 @@
+# cluster_inference
+
+Repo to do LabelBuddy annotations of a corpus of fMRI literature.
+This corpus consists of the open-access portion of NeuroQuery papers that conatain fMRI in the title or abstract.
+
+## Papers
+### How the papers were obtained
+We rand a script with this code:
+```bash
+#!/bin/bash
+
+pubget run --pmcids_file pmcids_for_open_fmri_papers.txt \
+    --fit_neuroquery                                          \
+    --labelbuddy                                              \
+    --nimare                                              \
+    ~/data/pubget_data
+```
+
+The `pmcids_for_open_fmri_papers.txt` file is found in the current directory.
+It contains the pmcids for all the papers in the `neuroquery` dataset that could be found on PubMed Central (i.e., that were open access).
+
+
+### Where the full papers are stored
+The full pubget output is stored on OSF: [https://osf.io/gukw2](https://osf.io/gukw2).
+
+
+## Annotations
+### File(s) being annotated: 
+- `/projects/cluster_inference/documents/documents.jsonl`
+  - corresponding file in the pubget output: 
+    - `cluster_inference/pmcidList_a84871e6b29a46f53d30d0463f66407f/subset_allArticles_labelbuddyData/documents00001.jsonl`
+
+### Annotation labels:
+- smoothing_snippet
+- cluster_thresh_used
+- cluster_thresh_in_voxels
+- cluster_thresh_in_mm
+- nonparametric_cluster_thresh
+- info_removed_in_name_extract
+- is_annotated
+- annotation_in_progress
+- discard_this_paper 
+
+### Labels found in other projects as well:
+- `<label2>`
+
+### Instructions for annotators
+`<description>`
+
+