JISCMail - FSL Archives

Thanks, Michael. that helps a lot.

So just in case others are interested

the first value is actually 75% of the median intensity of masked functional volumes

the second value is the smoothing kernel (in my case it was 5mm) divided by 2.355.

Best,

Tony

From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Harms, Michael [[log in to unmask]]
Sent: Tuesday, January 14, 2014 4:37 PM
To: [log in to unmask]
Subject: Re: [FSL] help with feat command line

Hi,

You can search for 'susan' in $FSLDIR/tcl/featlib.tcl, locate the line with the relevant command, and then trace back in the featlib.tcl code to figure out exactly how the values are derived.

cheers,

-MH

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: [log in to unmask]

From: Tony Jiang <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, January 14, 2014 2:04 PM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: [FSL] help with feat command line

Hi, All

can someone tell me how the parameters were determined based on a feat job for susan command line?

I see the command run from the log webpage. but i couldn't figure out how the two values were computed.

I have copy&pasted part of the log here. the two values were highlighted in red (the line calls up susan command)

Thanks

Tony

/usr/share/fsl/5.0/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 512.334900

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_bet -thr 51.23349 -Tmin -bin mask -odt char

/usr/share/fsl/5.0/bin/fslstats prefiltered_func_data_st -k mask -p 50
419.969757

/usr/share/fsl/5.0/bin/fslmaths mask -dilF mask

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_st -mas mask prefiltered_func_data_thresh

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func

/usr/share/fsl/5.0/bin/susan prefiltered_func_data_thresh 314.97731775 2.12314225053 3 1 1 mean_func 314.97731775 prefiltered_func_data_smooth

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mul 23.8112383888 prefiltered_func_data_intnorm

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_intnorm -bptf 25.0 -1 prefiltered_func_data_tempfilt

/usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data

/usr/share/fsl/5.0/bin/fslmaths filtered_func_data -Tmean mean_func

The information in this transmission is intended for official use of the Kessler Foundation. It is intended for the exclusive use of the persons or entities to which it is addressed. If you are not an intended recipient or the employee or agent responsible for delivering this transmission to an intended recipient, be aware that any disclosure, dissemination, distribution or copying of this communication, or the use of its contents, is strictly prohibited. If you received this transmission in error, please notify the sender by return e-mail and delete the material from any computer.

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.