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

Run multiple BrainVoyager instances on Mac OSX

On Mac OSX, it is not possible to run multiple BrainVoyager instances by click the dock icon. This can be done by writing two command lines in terminal as shown in Brainvoyager support website;

http://support.brainvoyager.com/installation-introduction/81-platform-related-remarks/331-run-multiple-brainvoyager-instances-on-mac-osx.html

Depending on the previous method I wrote an applescript*, using this script you don't have to write any thing you will use mouse clicks only. You have to click that applescript file at every time you want run more Brainvoyager instances, It can be added to the dock. 

Please click here to download the applescript app

* This applescript will work with local HASP only!

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

Related links

Brainvoyager QX tips and tricks 1; Some visualization tips

Brainvoyager QX tips and tricks 2; Create a 3d shape by drawing a region of interest

Create an averaged brain in Brainvoyager QX

Brainvoyager QX; rename DICOM files in multiple folders at once

Autoscale of vmr files (Brainvoyager QX) & automation of Advanced segmentation tools

Synchronizing E-prime with an MRI scanner

In the following pictures, you will see how we can synchronize E-prime with MRI scanner. So E-prime will start stimuli presentation using scanner pulse. you can download this E-prime file (Block.es) and modify it for your use.

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

mri_convert_multidata

This script helps automate mri_convert command in freesurfer for large set of data 

For download
Multi_mri_convert

http://www.freesurfer.net/fswiki/Easyfreesurfer


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

Related links

Easyfreesurfer

Using applescript to convert freesurfer stats2table (asegstats2table & aparcstats2table)

Using bash script to convert freesurfer stats2table (asegstats2table & aparcstats2table)

Easyfreesurfer

Easyfreesurfer is a simple script which was written to simplify and automate most freesurfer processes. It controls some commands such as; recon-all and mri_convert without writing any command in terminal, as user will only need to use mouse to select options and click buttons. This applescript works with both shell types bash and tcsh but it is suitable for Mac OS X only.

For download click here

http://www.freesurfer.net/fswiki/Easyfreesurfer

For using bash script, which works on both Linux and MAC, user needs to copy this script to data directory and execute it from there. 

Bash script works on bash shell only where "chmod +x" command used to make it executable as following;

chmod +x easyfreesurfer_bash.command 

or

chmod +x easyfreesurfer_bash.sh

Easyfreesurfer_bash.zip

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

Related links

mri_convert_multidata

Using applescript to convert freesurfer stats2table (asegstats2table & aparcstats2table)

Using bash script to convert freesurfer stats2table (asegstats2table & aparcstats2table)

Brainvoyager QX tips and tricks 2; Create a 3d shape by drawing a region of interest

In the following slides, I will present a simple method of creating a 3d mesh from a region of interest using draw with mouse tool.

First of all, open any *.vmr file, when you click on 3D volume tools, choose segmentation tab as shown in the following image. Tick enable for draw with mouse option (I selected 2D in-plane) because I drew a region of interest around corpus callosum. If you want to draw a multislice volume you can choose 3D (cube) but with care as you move from slide to another. To change draw tool color you should change (New) value in rage (225-240). I got orange color by change value to 226.

You can start drawing by selecting (ctrl+left click in windows) and (cmd+mouse left click in MAC).

After finishing drawing, click on 3D volume tools then choose segmentation tab and option as shown in the following image. Next steps are shown in the following series images.

Then select mesh morphing to smooth resulted shape.

In the final step, we save resulted mesh

We can combine two meshes by adding another mesh as shown in the following image.

Related links

Brainvoyager QX tips and tricks 1; Some visualization tips

Run multiple BrainVoyager instances on Mac OSX

Create an averaged brain in Brainvoyager QX

Brainvoyager QX; rename DICOM files in multiple folders at once

Autoscale of vmr files (Brainvoyager QX) & automation of Advanced segmentation tools

Brainvoyager QX tips and tricks 1; Some visualization tips

This entry is part of my talk about advanced features of visualization in Brain Voyage QX which was held in May 2008 at MARIARC, Liverpool.

I used BVQX (1.9.10). There are some differences between different versions, so please take this issue in account if you use another version. Hopefully, this could help!

Before starting; you have to refer to BrainVoyager QX Getting Started Guide
BrainVoyager QX Getting Started Guide

1- Sphere Mapping (Cortex-based alignment)

This can be done faster and easier in an automated way using a script provided through brain voyager QX support site by Draulio de Araujo. However, I am showing the normal method here.

2- Illustration of Brodmann areas, lobes, sulcus and gyruses...(on mesh)

Sphere Mapping should be processed before starting this step. Doing all of the previous steps ending with folding the (...RECOSM.srf) mesh by setting standard sphere vertices (image 7).

You should load a patch of interest from database that located in Atlas Brains folder in Brain voyager QX directory.

3- Illustration of Brodmann areas on 3D view; SAG, COR, AND TRA 

You should download  brodma.voi from Brain voyager user forums. or email me if you want a copy. (This file is available in the newest versions (Brainvoyager QX 2.x.x).

4- Drawing region on a mesh

In the following step, you should use ctrl and mouse click in order to draw a region of interest.When you finish drawing a closed curve you can toggle to fill mode and fill the region.

5- Representation of demarcated region on a polygon mesh

Related links

Brainvoyager QX tips and tricks 2; Create a 3d shape by drawing a region of interest

Run multiple BrainVoyager instances on Mac OSX

Create an averaged brain in Brainvoyager QX

Brainvoyager QX; rename DICOM files in multiple folders at once

Autoscale of vmr files (Brainvoyager QX) & automation of Advanced segmentation tools

Create an averaged brain in Brainvoyager QX

Regional differences in sulcal and gyral topography can be used as disease indications such as in schizophrenia (Csernansky et al., 2008). In the previous video I showed how we can combine multiple aligned surfaces (.srf files) in one surface brain like the following image;

For combining multiple volumes (.vmr files), we use another function in BrainVoyager QX. This function can be accessed in two ways;

1- Through Volumes tab and mouse click on Combine 3D Data Sets... sub tab as shown in the following image.

2- By clicking on 3D Volume Tool then selecting Talairach tab then clicking Combine Data Sets... button as shown in the following image.

After selecting one of the previous options we will get window like the following one, we select wanted files and press on Average button.

The resulted average looks like the following image;

Related links

Brainvoyager QX tips and tricks 1; Some visualization tips

Brainvoyager QX tips and tricks 2; Create a 3d shape by drawing a region of interest

Run multiple BrainVoyager instances on Mac OSX

Brainvoyager QX; rename DICOM files in multiple folders at once

Autoscale of vmr files (Brainvoyager QX) & automation of Advanced segmentation tools

Using bash script to convert freesurfer stats2table (asegstats2table & aparcstats2table)

At the previous entry, I presented how we can use applescript to control asegstats2table and aparcstats2table commands in order to generate text/ascii tables of freesurfer stats data for all subjects in the directory at once. At this entry I will show how we can write a bash script to control both asegstats2table and aparcstats2table commands. This bash script can be used in both Mac OS X and Linux.

freesurferstats2table_bash.zip

The following script uses aparcstats2table and asegstats2table to extract cortical thickness, surface area and volume of manually defined regions of interest using stats files that resulted from qdec.

aparc2table_qdec.zip

http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table

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

Related links

Easyfreesurfer

Using applescript to convert freesurfer stats2table (asegstats2table & aparcstats2table)

mri_convert_multidata

Using applescript to convert freesurfer stats2table (asegstats2table & aparcstats2table)

This applescript can be used to control asegstats2table and aparcstats2table commands in order to generate text/ascii tables of freesurfer stats data for all subjects in the directory at once using 4 mouse clicks!

Please click on the link below to download script;

freesurferstats2table

This script is suitable for MAC only.

The following script uses aparcstats2table and asegstats2table to extract cortical thickness, surface area and volume of manually defined regions of interest using stats files that resulted from qdec.

stats2table_qdec.zip

The main purpose of this script is to simplify and automate conversion process because subjects’ IDs should be written with some options in the command line depending on freesurfer stats file. So users will not need to write any thing when they use this script instead of command line;

asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt

http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table

or

aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt

http://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table

To visit script page in Freesurfer website please click on the following link 

http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table

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

Related links

Easyfreesurfer

mri_convert_multidata

Using bash script to convert freesurfer stats2table (asegstats2table & aparcstats2table)