Batching FSL tools and utilities using Applescript "3" (fslsplit)

This script has been written to automate conversion of 4D images to series of 3D images using fslsplit utility. Thanks to Carolina Mendez Orellana for the idea of this script. To download this script please click on the following link FSL_SPLIT

fslsplit splits a 4D file in one of 4 dimensions (time, x, y, z)

fslsplit <input> [output_basename] [-t/x/y/z]
        -t : separate images in time (default)
       -x : separate images in the x direction
       -y : separate images in the y direction
       -z : separate images in the z direction


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

Related links

Batching FSL tools and utilities using Applescript "1" (BET)

Batching FSL tools and utilities using Applescript and bash script "2" (SIENAX)

Batching FSL tools and utilities using Applescript and bash script "4" (fslchfiletype) Analyze2Nifti--Nifti2Analyze

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

Flip left and right orientation and check image orientation in FSL

Batching FSL tools and utilities using Applescript and bash script "2" (SIENAX)

This script has been written to automate and simplify SIENAX tool (FSL) without writing any command line. User only needs to specify data directory and to select options at the beginning. To download this script please click on the following link

Applescript

I wrote a bash script to automate and simplify SIENAX tool. It works on both Linux and MAC, user needs to copy script to data directory and execute it from there. This script works on bash shell only where it can be executed using "chmod +x" command as following;

chmod +x sienax_bash.command or chmod +x sienax_bash.sh

Bash script


SIENAX estimates total brain tissue volume, from a single image, normalised for skull size. It calls a series of FSL programs: It first strips non-brain tissue, and then uses the brain and skull images to estimate the scaling between the subject's image and standard space. It then runs tissue segmentation to estimate the volume of brain tissue, and multiplies this by the estimated scaling factor, to reduce head-size-related variability between subjects.




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

Related links

Batching FSL tools and utilities using Applescript "1" (BET)

Batching FSL tools and utilities using Applescript "3" (fslsplit)

Batching FSL tools and utilities using Applescript and bash script "4" (fslchfiletype) Analyze2Nifti--Nifti2Analyze

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

Flip left and right orientation and check image orientation in FSL

Batching FSL tools and utilities using Applescript "1" (BET)

I wrote this script to automate and simplify BET tool (FSL) without writing any command line. User only needs to specify data directory and to select options at the beginning. To download this script please click on the following link

BET script

BET (Brain Extraction Tool) deletes non-brain tissue from an image of the whole head. It can also estimate the inner and outer skull surfaces, and outer scalp surface, if you have good quality T1 and T2 input images.



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

Related links

Batching FSL tools and utilities using Applescript and bash script "2" (SIENAX)
Batching FSL tools and utilities using Applescript "3" (fslsplit)

Batching FSL tools and utilities using Applescript and bash script "4" (fslchfiletype) Analyze2Nifti--Nifti2Analyze

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

Flip left and right orientation and check image orientation in FSL