Friday 13 January 2012

Batching FSL tools and utilities using Applescript "5" (FIRST)

FIRST is a model-based segmentation/registration tool. It segment subcortical brain regions using Bayesian shape & appearance models. For further reading please visit the following link
http://www.fmrib.ox.ac.uk/fsl/first/index.html
The following script has been written to automate and simplify all five steps and two Quality Assurance processes. Click her to download script.

Please leave your feedback if you like this tool or a suggestion if you think it needs to be improved!

Related links

6 comments:

cvalencia said...

In which software did you get these beautiful images?

Jamaan Alghamdi said...

I created them using FIRST tool (FSL).

Mak said...

Hi, I found the software really useful! Thanks so much for building this.

I noticed that the output of the run_first_all had outputs like these:

vt_t1_all_none_firstseg.nii.gz
vt_t1_all_none_origsegs.nii.gz
vt_t1_to_std_sub.nii.gz

is there supposed to be "FAST" instead of "none"? as a result, I could not check my segmentations.

Jamaan Alghamdi said...

Hi Mak,

Thank you very much for using this script and for commenting here, telling me about this issue. Word "FAST" will not make any change, I will adapt script to be compatible with your files names and send it to you by email and will change the original one.

Jamaan

Mak said...

Thank you so much! Is there a place for me to check the volume for the subcortical structures so that I could at least be sure that my volumes segmented from FSL FORST are not unusually large or small? Thank you so much! my email: elijahmak@gmail.com

Jamaan Alghamdi said...

Hi Mak,

I understood that you already had created volume using fslstats command, is that right?

Regarding your previous comment about output file name "vt_t1_all_none_firstseg.nii.gz", could you please verify which did you use for for first run "All or a proper structure"

To find out why you get this name, could you please send one file, so I can test it.

Jamaan