From 06a36a06841d23b0ebe8b8c63aaab48469260e6d Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Tue, 14 Jul 2020 18:00:10 +0100
Subject: [PATCH] DOC: fixed a bug in the documentation identified by Chris
---
fsl/utils/filetree/__init__.py | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/fsl/utils/filetree/__init__.py b/fsl/utils/filetree/__init__.py
index 736ad9998..64db56916 100644
--- a/fsl/utils/filetree/__init__.py
+++ b/fsl/utils/filetree/__init__.py
@@ -230,17 +230,21 @@ altering this behaviour is again as simple as altering the FileTree to something
::
raw_data
- {subject}
- [ses-{session}]
+ {subject} (input_subject_dir)
+ [ses-{session}] (input_session_dir)
T1w.nii.gz
processed_data
- {subject}
- [ses-{session}]
+ {subject} (output_subject_dir)
+ [ses-{session}] (output_session_dir)
bet
{subject}[_{session}]_T1w_brain.nii.gz (bet_output)
{subject}[_{session}]_T1w_brain_mask.nii.gz (bet_mask)
Note that we also encoded the subject and session ID in the output filename.
+We also have to explicitly assign short names to the subject and session directories,
+even though we don't explicitly reference these in the script.
+The reason for this is that each directory and filename template must have a unique short name and
+in this case the default short names (respectively, "{subject}" and "[ses-{session}]") would not have been unique.
Some tools like FSL's FAST produce many output files. Rather than entering all
of these files in our FileTree by hand you can include them all at once by including `Sub-trees`_:
@@ -248,12 +252,12 @@ of these files in our FileTree by hand you can include them all at once by inclu
::
raw_data
- {subject}
- [ses-{session}]
+ {subject} (input_subject_dir)
+ [ses-{session}] (input_session_dir)
T1w.nii.gz
processed_data
- {subject}
- [ses-{session}]
+ {subject} (output_subject_dir)
+ [ses-{session}] (output_session_dir)
bet
{subject}[_{session}]_T1w_brain.nii.gz (bet_output)
{subject}[_{session}]_T1w_brain_mask.nii.gz (bet_mask)
--
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