Neuroimaging Made Easy Blog Releases

easy_neuroimage Easyfreesurfer

jamaan@www.nitrc.org (Jamaan Alghamdi) — Wed, 08 Feb 2012 18:36:00 GMT

<div style="font-size: 13px; text-align: left;">[color=#444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; line-height: 18px]<font color="#444444; font-family: arial, sans-serif; font-size: 13px; line-height: 18px">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.[/color]</font><div style="font-size: 13px; text-align: left;">[color=#444444; font-family: arial, sans-serif; font-size: 13px; line-height: 18px]
[/color][b][u]http://www.easyneuroimaging.com/2011/11/easyfreesurfer.html
[/u][/b]<div style="text-align: left;">[color=#444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; line-height: 18px]
<font color="#444444; font-family: arial, sans-serif; font-size: 13px; line-height: 18px">[url=http://www.freesurfer.net/fswiki/Easyfreesurfer]http://www.freesurfer.net/fswiki/Easyfreesurfer[/url][/color]</font><div style="text-align: left;"><div style="text-align: left;">[color=#444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; line-height: 18px]<font color="#444444; font-family: arial, sans-serif; font-size: 13px; line-height: 18px">[size= 10px]<p style="font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; padding: 0px; margin: 0px;"><font color="#333333; font-family: arial, helvetica, sans-serif; font-size: medium">[b]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. [/b][/color]<p style="margin: 0px;"> <p style="font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; padding: 0px; margin: 0px;">[color=#333333; font-family: arial, helvetica, sans-serif; font-size: medium][b]Bash script works on bash shell only where "chmod +x" command used to make it executable as following;[/b][/color]<p style="font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; padding: 0px; margin: 0px;">[color=#333333; font-family: arial, helvetica, sans-serif; font-size: medium][b]chmod +x easyfreesurfer_bash.command [/b][/color]<p style="font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; padding: 0px; margin: 0px;">[color=#333333; font-family: arial, helvetica, sans-serif; font-size: medium][b]or[/b][/color]<p style="font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; padding: 0px; margin: 0px;">[color=#333333; font-family: arial, helvetica, sans-serif; font-size: medium][b]chmod +x easyfreesurfer_bash.sh[/b][/color]<p style="font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; padding: 0px; margin: 0px;">[color=#333333; font-family: arial, helvetica, sans-serif; font-size: medium][b]
[/b][/color][/size]</font></font>

easy_neuroimage Convert freesurfer asegstats2table & aparcstats2table for multiple subjects

jamaan@www.nitrc.org (Jamaan Alghamdi) — Wed, 08 Feb 2012 18:28:00 GMT

<div class="paragraph_style_1" style="color: black; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 18px; opacity: 1; padding-bottom: 0px; padding-top: 0pt; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;">[color=#444444; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; line-height: 18px]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![/color]<div class="paragraph_style_1" style="color: black; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 18px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;"><div class="paragraph_style_2" style="color: #0433ff; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 18px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;">[color=#444444; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; line-height: 18px]<font color="black"> [/color]</font><strong style="font-weight: 400;">http://www.easyneuroimaging.com/2011/03/freesurferstats2table.html[/b]
<div style="margin: 0px;"><div style="margin: 0px;">[color=#38761d][b][i]This script is suitable for MAC only.[/i][/b][/color]<div style="margin: 0px;">[color=#38761d][b][i]
[/i][/b][/color]<div class="paragraph_style_1" style="color: black; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 18px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;">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;

<div class="paragraph_style_3" style="color: #ff2600; font-family: Courier, serif; font-size: 10px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 12px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;">asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt<div class="paragraph_style_1" style="color: black; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 18px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;">[url=http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table]http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table[/url]<div class="paragraph_style_1" style="color: black; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 18px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;"><div class="paragraph_style_1" style="color: black; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 18px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;">or<div class="paragraph_style_1" style="color: black; font-family: Times-Roman, Times, 'Times New Roman', serif; font-size: 15px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 18px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;"><div class="paragraph_style_3" style="color: #ff2600; font-family: Courier, serif; font-size: 10px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: 0px; line-height: 12px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;">aparcstats2table --subjects bert ernie fred margaret --hemi rh --meas thickness --tablefile aparc_stats.txt<div class="paragraph_style_1" style="font-family: Times-Roman, Times, 'Times New Roman', serif; font-style: normal; font-variant: normal; letter-spacing: 0px; line-height: 18px; opacity: 1; padding-bottom: 0px; padding-top: 0px; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; margin: 0px;"><div style="color: black; font-size: 15px; font-weight: 400;">[url=http://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table]http://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table[/url]<div style="color: black; font-size: 15px; font-weight: 400;"><div style="color: black;">[b]To visit script page in Freesurfer website please click on the following link[/b]<div style="font-size: 15px; font-weight: 400;"><div style="color: black;">[url=http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table]http://surfer.nmr.mgh.harvard.edu/fswiki/freesurferstats2table[/url]<div style="color: black;"><div style="color: black;"><p style="font-weight: 400; font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; margin: 0px;"> <p style="font-weight: 400; font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; margin: 0px;"> <p style="font-weight: 400; font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; margin: 0px;">[color=#333333; font-family: arial, helvetica, sans-serif; line-height: normal; font-size: medium][b]But in bash script, which works on both Linux and MAC, user needs to copy this script to data directory and execute it from there. [/b][/color]<span style="border-collapse: collapse; color: #222222; font-family: arial, sans-serif; font-size: 13px; line-height: normal;"><span style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px;"><span style="border-collapse: collapse; color: #222222; font-family: arial, sans-serif; font-size: 13px;">If you will use </span><span style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px;">[color=#ff0000]stats2table_bash.command[/color]</span><span style="border-collapse: collapse; color: #222222; font-family: arial, sans-serif; font-size: 13px;"> file copy it to your subjects' directory then execute it using </span></span>[color=#ff0000]stats2table_bash.command[/color]</span><span style="border-collapse: collapse; color: #222222; font-family: arial, sans-serif; font-size: 13px;">. with </span><span style="border-collapse: collapse; color: #222222;">[color=#3333ff]stats2table_bash.sh[/color]</span><span style="border-collapse: collapse; color: #222222; font-family: arial, sans-serif; font-size: 13px;"> you can do the same thing but you cant double click </span><span style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px;">[color=#3333ff]stats2table_bash.sh[/color]</span><span style="border-collapse: collapse; color: #222222; font-family: arial, sans-serif; font-size: 13px;">. </span>

easy_neuroimage Multiple DICOM to NIfTI converter using dcm2nii

jamaan@www.nitrc.org (Jamaan Alghamdi) — Wed, 08 Feb 2012 18:18:00 GMT

<div style="text-align: left;"><div style="text-align: center;"><div style="color: #444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px; margin: 0px;"><div style="text-align: left;"><span style="font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px;">dcm2nii is used to convert from DICOM format to various data format such as; </span><div style="color: #444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px; margin: 0px;"><div style="text-align: left;"><span style="font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px;">Compressed 4D NIfTI nii.gz, 4D NIfTI nii, 3D NIfTI hdr/img and 3D Anlyze hdr/img. Or even it modify </span><span style="font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px;">NIfTI format. There are two versions; the dcm2niigui and command line dcm2nii. This software was </span><span style="font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px;">written by Dr. Chris Rorden. It can be downloaded with mricron package;</span>
https://www.nitrc.org/projects/mricron/
<div style="color: #444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px; margin: 0px;"><div style="text-align: left;">
<div style="color: #444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px; margin: 0px;"><div style="text-align: left;"><div style="color: #444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px; margin: 0px;"><div style="text-align: left;"><div style="color: #444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px; margin: 0px;"><div style="text-align: left;">[color=#0433ff; font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px][/color]<div style="margin: 0px;"><div style="text-align: left;">[color=#0433ff; font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px]<span class="style_2" style="font-family: ArialMT, Arial, sans-serif; font-size: 11px; font-style: normal; font-weight: 400; line-height: 12px;">[url=http://www.cabiatl.com/mricro/mricron/dcm2nii.html][/url]</span>[/color]<span style="font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px; color: #000000;">MAC gui version is user friendly but it can convert one data set at a time. </span><div style="text-align: left;">[color=#000000]<span style="font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px;">Therefore, I wrote an </span>[/color]<span style="font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px;">applescript to convert multiple DICOM data sets to <span class="style_3" style="line-height: 17px; opacity: 1;">NIfTI/Analyze format at one instance using </span>dcm2nii command<span class="style_3" style="line-height: 17px; opacity: 1;">.</span></span><div style="text-align: left;"><div style="text-align: left;"><span style="font-family: ArialMT, Arial, sans-serif; font-size: 15px; line-height: 17px;"><span class="style_3" style="line-height: 17px; opacity: 1;"><div style="text-align: left;">Bash script works on both Linux and MAC.<div style="text-align: left;">user needs to copy this script to data directory and execute it from there using chmod +x to make it executable as following;<div style="text-align: left;">chmod +x dicom2nii.command or chmod +x dicom2nii.sh <div style="text-align: left;"><div style="text-align: left;">If you will use dicom2nii.command file copy it to your subjects' directory then execute it using dicom2nii.command. dicom2nii.sh you can do the same thing but you cant double click dicom2nii.sh.<div style="text-align: left;"><div style="text-align: left;">Note: If mricron directory is not **** /Applications/mricronmac ****<div style="text-align: left;">Please do not forget to change it in **dicom2nii.command** or **dicom2nii.command** using any text editor</span></span>

easy_neuroimage Analyze2Nifti and Nifti2Analyze using fslchfiletype

jamaan@www.nitrc.org (Jamaan Alghamdi) — Fri, 10 Feb 2012 10:24:00 GMT

[color=#444444; line-height: 18px]<font color="#444444; font-family: Arial, Helvetica, sans-serif; font-size: 13px; line-height: 18px">[b]This script has been written to automate FSL utility (fslchfiletype). Using this script user could convert multiple images at once using a few mouse click. There are six options; [/b][/color]</font>
<span style="font-family: Arial, Helvetica, sans-serif; font-size: large;">[b]<span style="line-height: 18px;">Analyze (img) <---> </span>Nifti (nii)[/b]</span>
<span style="font-family: Arial, Helvetica, sans-serif; font-size: large;">[b]Analyze (img) <---> compressed Nifti (nii.gz)[/b]</span>
<span style="font-family: Arial, Helvetica, sans-serif; font-size: large;">[b]Nifti (nii) <---> compressed Nifti (nii.gz)[/b]</span>

[color=#333333; font-family: arial, helvetica, sans-serif; font-size: medium]<p style="font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; padding: 0px; margin: 0px;">[b]But in bash script, which works on both Linux and MAC, user needs to copy this script to data directory and execute it from there. [/b]<p style="font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; padding: 0px; margin: 0px;">[b]Bash script works on bash shell only where "chmod +x" command used to make it executable as following;[/b][/color]<p style="font-family: arial, helvetica, sans-serif; font-size: medium; color: #333333; line-height: 16px; font: normal normal normal 16px/normal Arial; padding: 0px; margin: 0px;">[color=#333333; font-family: arial, helvetica, sans-serif; font-size: medium][b]chmod +x Analyze2Nifti-Nifti2Analyze.command or chmod +x Analyze2Nifti-Nifti2Analyze.sh[/b][/color]
[color=#0000ff; font-family: Arial, Helvetica, sans-serif; line-height: 18px; font-size: large][b][url=http://www.easyneuroimaging.com/2012/01/batching-fsl-tools-and-utilities-using.html]http://www.easyneuroimaging.com/2012/01/batching-fsl-tools-and-utilities-using.html[/url][/b][/color]
[color=#0000ff; font-family: Arial, Helvetica, sans-serif; line-height: 18px; font-size: large][b] [/b][/color]
[u][color=#0000ff; font-family: Arial, Helvetica, sans-serif; line-height: 18px; font-size: large][b][url=http://www.youtube.com/watch?v=N6S1zm4qecM]<font color="#000000"><font color="#000000">To watch the discription clip please visit this [/color]</font>youtube link[/url][/b]</font>[/u]
[b]
[/b]

easy_neuroimage FSL tool SIENAX for multi images

jamaan@www.nitrc.org (Jamaan Alghamdi) — Tue, 14 Feb 2012 4:08:00 GMT

<span style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; line-height: 18px; font-size: medium;">[b]These scripts have been written to automate and simplify SIENAX tool (FSL) without writing any command line. In applescript, user only needs to specify data directory and to select options at the beginning.[/b]</span><font face="Arial, Tahoma, Helvetica, FreeSans, sans-serif" size="3"><span style="line-height: 18px;">[b]
[/b]</span></font><p class="line867" style="font-family: Arial, 'Lucida Grande', sans-serif; font-size: 16px; font-weight: normal; line-height: normal; padding: 0px; margin: 0px;"><span style="font-weight: 800;"> </span><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 16.0px Arial;">[b]But in bash script, which works on both Linux and MAC, user needs to copy this script to data directory and execute it from there. [/b]<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 16.0px Arial;">[b]Bash script works on bash shell only where "chmod +x" command used to make it executable as following;[/b]<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 16.0px Arial;">[b]chmod +x sienax_bash.command or chmod +x sienax_bash.sh[/b]

<span style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; line-height: 18px; font-size: medium;">[b][url=http://www.easyneuroimaging.com/2011/12/batching-fsl-tools-using-applescript-2.html]http://www.easyneuroimaging.com/2011/12/batching-fsl-tools-using-applescript-2.html[/url][/b]</span>

easy_neuroimage FSL tool BET for multi images release

jamaan@www.nitrc.org (Jamaan Alghamdi) — Wed, 08 Feb 2012 18:39:00 GMT

<div style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; margin: 0px;">[color=#444444; font-size: 13px; line-height: 18px]<span style="font-family: Times, 'Times New Roman', serif;">[b]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. [/b][b]To download this script please click on the following link[/b]</span>[/color]<span style="font-family: Times, 'Times New Roman', serif;">
</span>
http://www.easyneuroimaging.com/2011/12/batching-bet-tool-fsl-using-applescript.html
[color=#444444; font-size: 13px; line-height: 18px]
[/color][color=#444444; font-size: 13px; line-height: 18px]<span style="font-family: Times, 'Times New Roman', serif;">[b][color=blue][url=http://www.fmrib.ox.ac.uk/fsl/bet2/index.html]<span style="color: blue;">BET[/color][/url]</span>[/b]</span>[/color][b] [/b](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 [i]and[/i] T2 input images.

easy_neuroimage FSL utility fslsplit for multi images

jamaan@www.nitrc.org (Jamaan Alghamdi) — Tue, 14 Feb 2012 4:03:00 GMT

[color=#444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px]<span style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; line-height: 18px;">[b]This script has been written to automate conversion of 4D [/b][/color]<span style="line-height: 18px;">[b]<span style="font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif;">images to series of 3D images using fslsplit utility</span><span style="font-family: Arial, Helvetica, sans-serif;">.</span>[/b]</span></span>

[color=#444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px]<span style="line-height: 18px;">[b]<span style="font-family: Arial, Helvetica, sans-serif;">[url=http://www.easyneuroimaging.com/2011/12/batching-fsl-tools-and-utilities-using.html]http://www.easyneuroimaging.com/2011/12/batching-fsl-tools-and-utilities-using.html[/url][/color][/b]</span></span>

easy_neuroimage FSL image_check/flip

jamaan@www.nitrc.org (Jamaan Alghamdi) — Mon, 13 Feb 2012 3:13:00 GMT

[color=#444444; font-family: Times, 'Times New Roman', serif; font-size: 13px; line-height: 18px]FSL image_flip/check is an applescript that written to flip left and right orientation of group of brain images. It can be used as well for checking image orientation of group of images in sequence where presentation of each image lasts for a proper time (defined by user; 10 seconds as an example).[/color]

<span style="font-family: Times, 'Times New Roman', serif; font-size: 13px; line-height: 18px;">[url=http://www.easyneuroimaging.com/2012/01/fsl-imageflipcheck-is-applescript-that.html] http://www.easyneuroimaging.com/2012/01/fsl-imageflipcheck-is-applescript-that.html[/url]</span>

[color=#444444]<span style="line-height: 18px;">
</span>[/color]

easy_neuroimage FSL tools (FIRST)

jamaan@www.nitrc.org (Jamaan Alghamdi) — Thu, 09 Feb 2012 22:46:00 GMT

[b][color=#444444; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px]<span style="font-family: Arial, Helvetica, sans-serif;">FIRST is </span>[/color]<span style="font-family: Arial;">a model-based segmentation/registration tool</span><span style="font-family: Arial, Helvetica, sans-serif;"><span>. It </span></span><span style="font-family: Arial, Helvetica, sans-serif;">segment </span><span style="font-family: Arial, Helvetica, sans-serif;">subcortical brain</span><span style="font-family: Arial, Helvetica, sans-serif;"> regions using Bayesian shape & appearance models. For further reading please visit the following link</span>
[color=blue; font-family: Arial, Helvetica, sans-serif][url=http://www.fmrib.ox.ac.uk/fsl/first/index.html]http://www.fmrib.ox.ac.uk/fsl/first/index.html[/url][/color]
<span style="font-family: Times, 'Times New Roman', serif;">The following script has been written to automate and simplify all five steps and two Quality Assurance processes</span><span><span style="font-family: Times, 'Times New Roman', serif;">.</span> </span>[/b]
[url=http://www.easyneuroimaging.com/2012/01/batching-fsl-tools-and-utilities-using_13.html]http://www.easyneuroimaging.com/2012/01/batching-fsl-tools-and-utilities-using_13.html[/url]
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[u][url=http://www.youtube.com/watch?v=QSnjfr9X1to][color=#333333; font-family: arial, helvetica, sans-serif; line-height: 16px; font-size: medium]<font color="#0000ff; font-family: Arial, Helvetica, sans-serif; line-height: 18px; font-size: large">[b]<font color="#000000">To watch the discription clip please visit this[/color][/b]</font></font>[color=#333333; font-family: arial, helvetica, sans-serif; line-height: 16px; font-size: medium][b]<font color="#000000"> youtube link[/color][/b]</font>[/url][/u]