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}
- modality
+ modality
@@ -105,6 +107,7 @@ The name for the datatype depends on the recording modality.
microscopy
NIRS
motion
+ MRS
anat
@@ -114,6 +117,7 @@ The name for the datatype depends on the recording modality.
micr
nirs
motion
+ mrs
func
@@ -123,6 +127,7 @@ The name for the datatype depends on the recording modality.
+
dwi
@@ -132,6 +137,7 @@ The name for the datatype depends on the recording modality.
+
perf
@@ -141,6 +147,7 @@ The name for the datatype depends on the recording modality.
+
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",
]