From e4d8e71363782d74fc83a84dfbfd9432e3d39763 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Thu, 4 Oct 2018 10:58:59 -0700
Subject: [PATCH] newlines

---
 ...ological_and_other_continous_recordings.md | 126 +++++++++---------
 .../05_behavioural_experiments.md             |  34 ++---
 2 files changed, 80 insertions(+), 80 deletions(-)

diff --git a/src/04_modality_specific_files/04_physiological_and_other_continous_recordings.md b/src/04_modality_specific_files/04_physiological_and_other_continous_recordings.md
index f0bbb83264..397fc08414 100644
--- a/src/04_modality_specific_files/04_physiological_and_other_continous_recordings.md
+++ b/src/04_modality_specific_files/04_physiological_and_other_continous_recordings.md
@@ -1,63 +1,63 @@
-# Physiological and other continuous recordings
-
-Template:
-```
-sub-<participant_label>/[ses-<session_label>/]
-    func/
-        <matches>[_recording-<label>]_physio.tsv.gz
-        <matches>[_recording-<label>]_physio.json
-        <matches>[_recording-<label>]_stim.tsv.gz
-        <matches>[_recording-<label>]_stim.json
-```
-
-Optional: Yes
-
-Where ``<matches>`` corresponds to task file name without the `_bold.nii[.gz]`` suffix. For example: `sub-control01_task-nback_run-1`. If the same continuous recording has been used for all subjects (for example in the case where they all watched the same movie) one file can be used and placed in the root directory. For example: `task-movie_stim.tsv.gz`
-
-Physiological recordings such as cardiac and respiratory signals and other continuous measures (such as parameters of a film or audio stimuli) can be specified using two files: a gzip compressed TSV file with data (without header line) and a JSON for storing start time, sampling frequency, and name of the columns from the TSV. Please note that in contrast to other TSV files this one does not include a header line. Instead the name of columns are specified in the JSON file. This is to improve compatibility with existing software (FSL PNM) as well as make support for other file formats possible in the future.  Start time should be expressed in seconds in relation to the time of start of acquisition of the first volume in the corresponding imaging file (negative values are allowed). Sampling frequency should be expressed in Hz. Recordings with different sampling frequencies and/or starting times should be stored in separate files. The following naming conventions should be used for column names:
-
-| Column name | Definition                                           |
-|:------------|:-----------------------------------------------------|
-| cardiac     | continuous pulse measurement                         |
-| respiratory | continuous breathing measurement                     |
-| trigger     | continuous measurement of the scanner trigger signal |
-
-Any combination of those three can be included as well as any other stimuli related continuous variables (such as low level image properties in a video watching paradigm).
-
-Physiological recordings (including eye tracking) should use the _physio suffix, and signals related to the stimulus should use _stim suffix. For motion parameters acquired from scanner side motion correction please use _physio suffix.
-
-More than one continuous recording file can be included (with different sampling frequencies). In such case use different labels. For example: _recording-contrast, _recording-saturation. The full file name could then look like this: sub-control01_task-nback_run-2_recording-movie_stim.tsv.gz
-
-For multi-echo data, physio.tsv file is applicable to all echos of particular run.
-For eg:
-```
-sub-01_task-cuedSGT_run-1_physio.tsv.gz
-sub-01_task-cuedSGT_run-1_echo-1_bold.nii.gz
-sub-01_task-cuedSGT_run-1_echo-2_bold.nii.gz
-sub-01_task-cuedSGT_run-1_echo-3_bold.nii.gz
-```
-
-Example:
-```
-sub-control01/
-    func/
-        sub-control01_task-nback_physio.tsv.gz
-```
-(after decompression)
-```
-34  110 0
-44  112 0
-23  100 1
-```
-```
-sub-control01/
-    func/
-        sub-control01_task-nback_physio.json
-```
-```JSON
-{
-   "SamplingFrequency": 100.0,
-   "StartTime": -22.345,
-   "Columns": ["cardiac", "respiratory", "trigger"]
-}
-```
\ No newline at end of file
+# Physiological and other continuous recordings
+
+Template:
+```
+sub-<participant_label>/[ses-<session_label>/]
+    func/
+        <matches>[_recording-<label>]_physio.tsv.gz
+        <matches>[_recording-<label>]_physio.json
+        <matches>[_recording-<label>]_stim.tsv.gz
+        <matches>[_recording-<label>]_stim.json
+```
+
+Optional: Yes
+
+Where ``<matches>`` corresponds to task file name without the `_bold.nii[.gz]`` suffix. For example: `sub-control01_task-nback_run-1`. If the same continuous recording has been used for all subjects (for example in the case where they all watched the same movie) one file can be used and placed in the root directory. For example: `task-movie_stim.tsv.gz`
+
+Physiological recordings such as cardiac and respiratory signals and other continuous measures (such as parameters of a film or audio stimuli) can be specified using two files: a gzip compressed TSV file with data (without header line) and a JSON for storing start time, sampling frequency, and name of the columns from the TSV. Please note that in contrast to other TSV files this one does not include a header line. Instead the name of columns are specified in the JSON file. This is to improve compatibility with existing software (FSL PNM) as well as make support for other file formats possible in the future.  Start time should be expressed in seconds in relation to the time of start of acquisition of the first volume in the corresponding imaging file (negative values are allowed). Sampling frequency should be expressed in Hz. Recordings with different sampling frequencies and/or starting times should be stored in separate files. The following naming conventions should be used for column names:
+
+| Column name | Definition                                           |
+|:------------|:-----------------------------------------------------|
+| cardiac     | continuous pulse measurement                         |
+| respiratory | continuous breathing measurement                     |
+| trigger     | continuous measurement of the scanner trigger signal |
+
+Any combination of those three can be included as well as any other stimuli related continuous variables (such as low level image properties in a video watching paradigm).
+
+Physiological recordings (including eye tracking) should use the _physio suffix, and signals related to the stimulus should use _stim suffix. For motion parameters acquired from scanner side motion correction please use _physio suffix.
+
+More than one continuous recording file can be included (with different sampling frequencies). In such case use different labels. For example: _recording-contrast, _recording-saturation. The full file name could then look like this: sub-control01_task-nback_run-2_recording-movie_stim.tsv.gz
+
+For multi-echo data, physio.tsv file is applicable to all echos of particular run.
+For eg:
+```
+sub-01_task-cuedSGT_run-1_physio.tsv.gz
+sub-01_task-cuedSGT_run-1_echo-1_bold.nii.gz
+sub-01_task-cuedSGT_run-1_echo-2_bold.nii.gz
+sub-01_task-cuedSGT_run-1_echo-3_bold.nii.gz
+```
+
+Example:
+```
+sub-control01/
+    func/
+        sub-control01_task-nback_physio.tsv.gz
+```
+(after decompression)
+```
+34  110 0
+44  112 0
+23  100 1
+```
+```
+sub-control01/
+    func/
+        sub-control01_task-nback_physio.json
+```
+```JSON
+{
+   "SamplingFrequency": 100.0,
+   "StartTime": -22.345,
+   "Columns": ["cardiac", "respiratory", "trigger"]
+}
+```
diff --git a/src/04_modality_specific_files/05_behavioural_experiments.md b/src/04_modality_specific_files/05_behavioural_experiments.md
index b32ddeb21c..a5adfd379f 100644
--- a/src/04_modality_specific_files/05_behavioural_experiments.md
+++ b/src/04_modality_specific_files/05_behavioural_experiments.md
@@ -1,17 +1,17 @@
-# Behavioral experiments (with no MRI)
-
-Template:
-```
-sub-<participant_label>/[ses-<session_label>/]
-    beh/
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_events.tsv
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_events.json
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_beh.tsv
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_beh.json
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_physio.tsv.gz
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_physio.json
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_stim.tsv.gz
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_stim.json
-```
-
-In addition to logs from behavioral experiments performed along imaging data acquisitions one can also include data from experiments performed outside of the scanner. The results of those experiments can be stored in the beh folder using the same formats for event timing (`_events.tsv`), metadata (`_events.json`), physiological (`_physio.tsv.gz`, `_physio.json`) and other continuous recordings (`_stim.tsv.gz`, `_stim.json`) as for tasks performed during MRI acquisitions. Additionally, events files that do not include the mandatory `onset` and `duration` columns can still be included, but should be labelled `_beh.tsv` rather than `_events.tsv`.
+# Behavioral experiments (with no MRI)
+
+Template:
+```
+sub-<participant_label>/[ses-<session_label>/]
+    beh/
+        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_events.tsv
+        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_events.json
+        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_beh.tsv
+        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_beh.json
+        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_physio.tsv.gz
+        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_physio.json
+        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_stim.tsv.gz
+        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_stim.json
+```
+
+In addition to logs from behavioral experiments performed along imaging data acquisitions one can also include data from experiments performed outside of the scanner. The results of those experiments can be stored in the beh folder using the same formats for event timing (`_events.tsv`), metadata (`_events.json`), physiological (`_physio.tsv.gz`, `_physio.json`) and other continuous recordings (`_stim.tsv.gz`, `_stim.json`) as for tasks performed during MRI acquisitions. Additionally, events files that do not include the mandatory `onset` and `duration` columns can still be included, but should be labelled `_beh.tsv` rather than `_events.tsv`.