diff --git a/docs/getting_started/folders_and_files/files.md b/docs/getting_started/folders_and_files/files.md index 7901b01e..2487ccc5 100644 --- a/docs/getting_started/folders_and_files/files.md +++ b/docs/getting_started/folders_and_files/files.md @@ -57,7 +57,7 @@ derivative data. ## Modalities -### MRI +### Magnetic Resonance Imaging #### `anat`: Anatomical MRI @@ -288,14 +288,16 @@ Template: 
sub-<label>/
     [ses-<label>/]
         perf/
-            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_asl.json
-            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_asl.nii[.gz]
-            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_m0scan.json
-            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_m0scan.nii[.gz]
+            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<mag|phase|real|imag>]_asl.json
+            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<mag|phase|real|imag>]_asl.nii[.gz]
+            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<mag|phase|real|imag>]_m0scan.json
+            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<mag|phase|real|imag>]_m0scan.nii[.gz]
             sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_aslcontext.tsv
             sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_asllabeling.jpg
             sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_asllabeling.png
             sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_asllabeling.tif
+            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_mod-<label>][_echo-<index>][_part-<mag|phase|real|imag>]_noRF.json
+            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_mod-<label>][_echo-<index>][_part-<mag|phase|real|imag>]_noRF.nii[.gz]
             sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_recording-<label>]_physio.json
             sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_recording-<label>]_physio.tsv.gz
             sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_recording-<label>]_stim.json
@@ -497,7 +499,7 @@ in which case those values are listed in <>, separated by 
 
 
-### `pet`
+### Positron Emission Tomography
 
 
 Template:
@@ -544,7 +546,7 @@ in which case those values are listed in <>, separated by 
 
 
-### `nirs`
+### Near Infra-Red Spectroscopy
 
 
 Template:
@@ -597,7 +599,7 @@ in which case those values are listed in <>, separated by 
 
 
-### `motion`
+### Motion
 
 
 Template:
@@ -643,3 +645,95 @@ in which case those values are listed in <>, separated by 
 
+
+
+### Magnetic Resonance Spectroscopy
+
+
+Template:
+
sub-<label>/
+    [ses-<label>/]
+        mrs/
+            sub-<label>[_ses-<label>][_task-<label>][_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>][_echo-<index>][_inv-<index>]_mrsi.json
+            sub-<label>[_ses-<label>][_task-<label>][_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>][_echo-<index>][_inv-<index>]_mrsi.nii[.gz]
+            sub-<label>[_ses-<label>][_task-<label>][_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>][_echo-<index>][_inv-<index>]_mrsref.json
+            sub-<label>[_ses-<label>][_task-<label>][_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>][_echo-<index>][_inv-<index>]_mrsref.nii[.gz]
+            sub-<label>[_ses-<label>][_task-<label>][_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>][_echo-<index>][_inv-<index>]_svs.json
+            sub-<label>[_ses-<label>][_task-<label>][_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>][_echo-<index>][_inv-<index>]_svs.nii[.gz]
+            sub-<label>[_ses-<label>][_task-<label>][_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>][_echo-<index>][_inv-<index>]_unloc.json
+            sub-<label>[_ses-<label>][_task-<label>][_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>][_echo-<index>][_inv-<index>]_unloc.nii[.gz]
+            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>]_events.json
+            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_nuc-<label>][_voi-<label>][_rec-<label>][_run-<index>]_events.tsv
+

+

+Legend:
+
    
+
  • 
+
    For more information about filename elements (for example, entities, suffixes, extensions),
+follow the links embedded in the filename template.
    
+
    • 
+
  • 
+
    Filename entities or directories between square brackets
+(for example, [_ses-<label>]) are OPTIONAL.
    
+
    • 
+
  • 
+
    Some entities may only allow specific values,
+in which case those values are listed in <>, separated by |.
    
+
    • 
+
  • 
+
    _<suffix> means that there are several (>6) valid suffixes for this filename pattern.
    
+
    • 
+
  • 
+
    .<extension> means that there are several (>6) valid extensions for this file type.
    
+
    • 
+
  • 
+
    [.gz] means that both the unzipped and gzipped versions of the extension are valid.
    
+
    • 
+

+
+

+
+
+
+### Microscopy
+
+
+Template:
+
sub-<label>/
+    [ses-<label>/]
+        micr/
+            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.<extension>
+            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>][_stain-<label>][_run-<index>][_chunk-<index>]_<suffix>.json
+            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>]_photo.jpg
+            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>]_photo.json
+            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>]_photo.png
+            sub-<label>[_ses-<label>]_sample-<label>[_acq-<label>]_photo.tif
+

+

+Legend:
+
    
+
  • 
+
    For more information about filename elements (for example, entities, suffixes, extensions),
+follow the links embedded in the filename template.
    
+
    • 
+
  • 
+
    Filename entities or directories between square brackets
+(for example, [_ses-<label>]) are OPTIONAL.
    
+
    • 
+
  • 
+
    Some entities may only allow specific values,
+in which case those values are listed in <>, separated by |.
    
+
    • 
+
  • 
+
    _<suffix> means that there are several (>6) valid suffixes for this filename pattern.
    
+
    • 
+
  • 
+
    .<extension> means that there are several (>6) valid extensions for this file type.
    
+
    • 
+
  • 
+
    [.gz] means that both the unzipped and gzipped versions of the extension are valid.
    
+
    • 
+

+
+

+
\ No newline at end of file
diff --git a/docs/getting_started/folders_and_files/folders.md b/docs/getting_started/folders_and_files/folders.md
index d7e462e6..c60349b1 100644
--- a/docs/getting_started/folders_and_files/folders.md
+++ b/docs/getting_started/folders_and_files/folders.md
@@ -68,6 +68,7 @@ Represents different types of data. Must be one of:
 -   `micr`: microscopy data
 -   `nirs`: near-infrared spectroscopy data
 -   `motion`: motion capture data
+-   `magnectic resonance spectroscopy`: motion capture data
 
 The name for the datatype depends on the recording modality.
 
@@ -87,12 +88,13 @@ The name for the datatype depends on the recording modality.
 .tg .tg-beh{border-color:#000000;color:var(--beh);font-size:18px; text-align:center;vertical-align:middle}
 .tg .tg-nirs{border-color:#000000;color:var(--nirs);font-size:18px; text-align:center;vertical-align:middle}
 .tg .tg-motion{border-color:#000000;color:var(--motion);font-size:18px; text-align:center;vertical-align:middle}
+.tg .tg-mrs{border-color:#000000;color:var(--mrs);font-size:18px; text-align:center;vertical-align:middle}
 
 
-    
+    
@@ -105,6 +107,7 @@ The name for the datatype depends on the recording modality.
     
+    
@@ -114,6 +117,7 @@ The name for the datatype depends on the recording modality.
     
+    
@@ -123,6 +127,7 @@ The name for the datatype depends on the recording modality.
     
+    
@@ -132,6 +137,7 @@ The name for the datatype depends on the recording modality.
     
+    
@@ -141,6 +147,7 @@ The name for the datatype depends on the recording modality.
     
+    

 
   

     modalitymodality
   

 
 
microscopy
     NIRS
     motionMRS
   

   

     anatmicr
     nirs
     motionmrs
   

   

     func

     
     
   

   

     dwi
     
     
   

   

     perf
     
     
   

 
 

diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
index 2b9b3aa7..994124de 100644
--- a/docs/stylesheets/extra.css
+++ b/docs/stylesheets/extra.css
@@ -7,7 +7,7 @@
     --beh: #fb9a99;
     --nirs: #b2df8a;
     --motion: #e31a1c;
-    --unused: #fdbf6f;
+    --mrs: #fdbf6f;
     --unused2: #ff7f00;
     --unused3: #cab2d6;
     --unused4: #ffff99;
diff --git a/requirements.in b/requirements.in
index 4a4398a9..4d888d07 100644
--- a/requirements.in
+++ b/requirements.in
@@ -1,5 +1,6 @@
 gender_guesser
 geopy
+markdown-it-py
 mkdocs-material[imaging]
 mkdocs-macros-plugin
 mkdocs-open-in-new-tab
diff --git a/requirements.txt b/requirements.txt
index bc792710..a361d1ce 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -89,12 +89,16 @@ markdown==3.6
     #   mkdocs
     #   mkdocs-material
     #   pymdown-extensions
+markdown-it-py==3.0.0
+    # via -r requirements.in
 markupsafe==2.1.5
     # via
     #   jinja2
     #   mkdocs
 matplotlib==3.9.0
     # via seaborn
+mdurl==0.1.2
+    # via markdown-it-py
 mergedeep==1.3.4
     # via
     #   mkdocs
diff --git a/tools/build/print_filename_templates.py b/tools/build/print_filename_templates.py
index 2d1405d7..3c8768e6 100644
--- a/tools/build/print_filename_templates.py
+++ b/tools/build/print_filename_templates.py
@@ -17,9 +17,11 @@
     "eeg",
     "ieeg",
     "meg",
-    "pet",
-    "nirs",
+    "micr",
     "motion",
+    "mrs",
+    "nirs",
+    "pet",
 ]