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Brainhack-Proceedings-2015 / ITO-AMX-LI

Calculating the Laterality Index Using FSL for Stroke Neuroimaging Data
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FSL scripts in http://github.com/npnl/LI_FSL ? #2

Open jbpoline opened 8 years ago

jbpoline commented 8 years ago

Hi,

I liked this work: useful especially when the matlab license is an issue.

GITHUB

NPNL GitHub ENIGMA Wrapper Scripts Laterality Index (LI) ASL Processing Tips DTI Processing Tips T2 Maps Read-Logfiles AFNI MRI Analysis SPM MRI Analysis PyMVPA Brain Voyager MRI Analysis FSL MRI Analysis

NEUROIMAGING TOOLS NITRC AFNI FSL NIPY

OPEN SOURCE NEUROSCIENCE & DATA SHARING Open Neuroscience INDI Database The Human Connectome Neurosynth BrainHack

I checked the two most promising: Laterality Index (LI) and FSL-MRI-Analysis but could not find the scripts to review and test them. Did I miss something ? apologies if I did. Also, is there an example dataset to test ?

npnl commented 8 years ago

Thank you for your helpful comments and drawing our attention to several things to fix. We have responded to them here: • I saw that in your report you state that "Our scripts for these calculations may be found online at http://chan.usc.edu/npnl/resources." and went to this address. I checked the two most promising: Laterality Index (LI) and FSL-MRI-Analysis but could not find the scripts to review and test them. Did I miss something? apologies if I did. Also, is there an example dataset to test? We thank the reviewer for pointing this out. We had the some of our scripts in a separate branch; however, now we have placed the scripts in a zipped folder on our brainhack page (https://github.com/npnl/LI-FSL) and have updated this in our markdown document (https://github.com/npnl/LI-FSL/blob/master/LI_Abstract/README.md).

To note: Currently, our scripts run in bash and in matlab; we are working on stream-lining our script into a script that uses python and bash, and will update the package on github in a couple of weeks once it is complete. We cannot put data online for testing but could provide data by request if emailed. We have, however, put some sample folders to demonstrate the file structure needed for the script to run (https://github.com/npnl/LI-FSL) • Other minor issues; you could discuss/implement the threshold free index that have been proposed, most recently in http://www.ncbi.nlm.nih.gov/pubmed/26846561 We appreciate this helpful advice. We have now reflected this change in the conclusion of our document. • minor as well: github does not render the table well. Not sure if there is an easy fix for that. We agree with the reviewer; however this seems to look ok once converted to the pdf version. For simplicity, we have now saved the table as a jpeg image and uploaded the file here as well: https://github.com/npnl/LI-FSL/blob/master/LI_Abstract/lli08ra.jpg

pbellec commented 8 years ago

@npnl it looks like you addressed all issues. Please close the issue if this is the case. @jbpoline let us know if there is anything missing.

npnl commented 8 years ago

Issues have been addressed; a stream-lined script using only bash has been uploaded to our own github page (https://github.com/npnl/LI-FSL) . Closing this issue.

jbpoline commented 8 years ago

thanks for addressing the issues JB