From 3b77bbcb7838389f9b688257a4c264a467c1f289 Mon Sep 17 00:00:00 2001 From: Gabriele Lohmann Date: Fri, 19 Jul 2024 15:35:36 +0200 Subject: [PATCH] added readme --- recipes/lipsia/README.md | 32 ++++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/recipes/lipsia/README.md b/recipes/lipsia/README.md index 5aabb25b..c5f95348 100644 --- a/recipes/lipsia/README.md +++ b/recipes/lipsia/README.md @@ -1,21 +1,45 @@ ---------------------------------- -## REPLACE_WITH_Name_of_Container/toolVersion ## -Short_description_of_container +## lipsia/toolVersion ## + Example: ``` +*Onesample test at the 2nd level* (`vlisa_onesample`_). +Example: the input is a set of contrast maps called "data_*.nii.gz":: + + vlisa_onesample -in data_*.nii.gz -mask mask.nii -out result.v + vnifti -in result.v -out result.nii + + +*Twosample test at the 2nd level* (`vlisa_twosample`_). +Example: input are two sets of contrast maps called "data1_*.nii.gz" and "data2_*.nii.gz":: + + vlisa_twosample -in1 data1_*.nii.gz -in2 data2_*.nii.gz -mask mask.nii -out result.v + vnifti -in result.v -out result.nii + + +*Single subject test (1st level)* (`vlisa_prewhitening`_). +Example: input are two runs acquired in the same session called "run1.nii.gz" and "run2.nii.gz". +Preprocessing should include a correction for baseline drifts!:: + + + vlisa_prewhitening -in run1.nii.gz run2.nii.gz -design des1.txt des2.txt -mask mask.nii -out result.v + vnifti -in result.v -out result.nii ``` -More documentation can be found here: link_to_documentation +More documentation can be found here: https://github.com/lipsia-fmri/lipsia To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml REPLACE_WITH_Name_of_Container/toolVersion Citation: ``` +Lohmann et al (2023) "Improving the reliability of fMRI-based predictions of intelligence via semi-blind machine learning", bioRxiv, https://doi.org/10.1101/2023.11.03.565485 + ``` -License: +License: BSD-3-Clause license + ----------------------------------