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FSL  December 2008

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Subject:

Re: Fugue -field map correction

From:

Matt Glasser <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 23 Dec 2008 14:47:35 -0600

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (176 lines)

Your dwell time seems rather high compared to the one I used.  Perhaps you
need to divide it by 1000 and try again?  I think it is measured in
milliseconds but fugue takes it in seconds.

Peace,

Matt.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Rajagopalan, Venkateswaran
Sent: Tuesday, December 23, 2008 1:31 PM
To: [log in to unmask]
Subject: Re: [FSL] Fugue -field map correction

Dear Mark,

Thanks for your kind information. I tried using Pre stats in FEAT GUI as per
your guidelines but I didn't get good results. I would like clarify with you
some of my doubts; 1) i chose only "pre-stats " from the top pull down menu
as a result of this the icons in the bottom which were enabled to do pre
stats operation are Misc, Data, Pres-stats and Registration, i unchecked the
option Balloon help and progress watcher under the "Misc" option. Then under
the data icon i loaded my DTI data set and chose an output folder to save my
results, here under the "Data" icon do i need to give the value of TR for my
EPI sequence and do i also need to specify the high pass filter cutoff
value. Then under "Pres stats" icon i chose B0 unwarping option and
unchecked all other options except FWHM like BET extraction , temporal
filtering etc then gave my field map image and BET extracted magnitude
image, dwell time and EPI TE time and chose my unwarp direction, i don't
know how to choose the %signal loss threshold any criteria available for
that currently i retained the default value of 10, then corresponding to
sigma of 0.5 i chose FWHM =2.35*0.5 ~1.2. Then i unchecked the default
checked Linear registration icon, is it correct to uncheck this registration
option or i have to leave it checked as such. 
I tried Matt's command line approach also but didn't get good results. I
repeated the above steps by changing the unwrap direction from y to -y but
once again i didn't get good results. One more doubt i want to clarify is
the end result "filtered_func_data" has intensity values which are very
large when compared to the original DTI image intensity whereas i didn't see
these large values in my final image when i followed Matt's approach.

I am sorry to bother you,

Thanks

Regards
venkateswaran
   


-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
Sent: Mon 12/22/2008 5:28 PM
To: [log in to unmask]
Subject: Re: [FSL] Fugue -field map correction
 
Hi,

The pre-processing of the fieldmap sounds fine.

The FEAT GUI is the best way to get fieldmap unwarping done as
it will do all the necessary registration steps (and some extra cleanup
of the fieldmap) for you automatically.  All you need to do is give it
your fieldmap in rad/s, the corresponding magnitude image (after
running BET on it to remove the non-brain structures) and some
parameter values (e.g. echo spacing).  It is all contained under
the "pre-stats" part and you can run it on your DTI images by
just selecting pre-stats only as the main option (top left pull-down
menu), using your DTI as the 4D input data, and turning off all the
other pre-stats options.  The output file will be called  
filtered_func_data
but will represent your distortion corrected EPI data.

That should work for you with your data.
If you have any trouble then let us know.

All the best,
	Mark



On 22 Dec 2008, at 22:19, Rajagopalan, Venkateswaran wrote:

>
> Dear All,
>
> I am new to field map correction. My field map data acquisition is a  
> single real field map image, gradient echo sequence. I have the  
> following images 1) EPI (for DTI),2)single real field map image in  
> units rad/sec and 3) the corresponding gradient echo magnitude  
> images. I went through FUGUE instruction manual and also through  
> PRELUDE documentation. There are few things which i am not able to  
> understand. I went through the field map processing steps mentioned  
> here http://www.fmrib.ox.ac.uk/fsl/fugue/feat_fieldmap.html and made  
> sure that my field map images meet the requirement for instance my  
> field map is a single real field map image registered with the  
> magnitude image (step 1b and c ), its units are in rad/sec  
> (confirmed with MR technician), i regularised them using gaussian  
> FWHM of 0.5 fugue --loadfmap=fieldmap_rads -s 1 -- 
> savefmap=fieldmap_regu. After this step i used the following FUGUE  
> command fugue -i epi --dwell=0.85 --loadfmap=fieldmap_regu -u  
> result. My first question is this approach correct.
>
> My Next question is, i have uploaded  the screenshot of my "result"  
> image  in the following link
http://www.beetony.com/uploads/venk/FUGUE_result.jpg 
>  where you can see the problem, i feel that this is due to the fact  
> that field map and EPI images are not registered. I don't know  
> whether FUGUE takes cares of the registration between the gradient  
> echo field map which is of dim 63*63*30 and epi (DTI) sequence dim  
> 127*127*30 or i have to register my fieldmap by distorting it using  
> FUGUE option "fugue -i undistortedimage -p unwrappedphase -- 
> dwell=dwelltime --asym=asymtime --nokspace -s 0.5 -w warpedimage"  
> and then register the two images together and then use the following  
> FUGUE option "fugue -i epi --dwell=0.85 --loadfmap=fieldmap_regu -u  
> result" where now epi and fieldmap_regu are brought into common space.
>
> I am sorry this may be a stupid question or approach kindly help me  
> with this.
>
> Thanks in advance,
>
> venkateswaran
>
>
> P Please consider the environment before printing this e-mail
>
>
>
> Cleveland Clinic is ranked one of the top hospitals
> in America by U.S. News & World Report (2008).
> Visit us online at http://www.clevelandclinic.org for
> a complete listing of our services, staff and
> locations.
>
>
> Confidentiality Note:  This message is intended for use
> only by the individual or entity to which it is addressed
> and may contain information that is privileged,
> confidential, and exempt from disclosure under applicable
> law.  If the reader of this message is not the intended
> recipient or the employee or agent responsible for
> delivering the message to the intended recipient, you are
> hereby notified that any dissemination, distribution or
> copying of this communication is strictly prohibited.  If
> you have received this communication in error,  please
> contact the sender immediately and destroy the material in
> its entirety, whether electronic or hard copy.  Thank you.
>



===================================

P Please consider the environment before printing this e-mail

Cleveland Clinic is ranked one of the top hospitals
in America by U.S. News & World Report (2008).  
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.


Confidentiality Note:  This message is intended for use
only by the individual or entity to which it is addressed
and may contain information that is privileged,
confidential, and exempt from disclosure under applicable
law.  If the reader of this message is not the intended
recipient or the employee or agent responsible for
delivering the message to the intended recipient, you are
hereby notified that any dissemination, distribution or
copying of this communication is strictly prohibited.  If
you have received this communication in error,  please
contact the sender immediately and destroy the material in
its entirety, whether electronic or hard copy.  Thank you.

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