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Subject:

Re: Fugue -field map correction

From:

"Rajagopalan, Venkateswaran" <[log in to unmask]>

Reply-To:

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

Date:

Mon, 29 Dec 2008 10:38:12 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (329 lines)

Dear Mark,

Thanks for your kind help. I followed your guidelines and got good results i.e my dti images are undistorted. Your advise to use report page and FSL's course material on FUGUE was very helpful to find out my mistakes. I made the following mistake that is i didn't use PRELUDE to unwrap the phase in the preliminary processing stage as mentioned in the FSL's FUGUE course material that solved the problem, i thought the PRELUDE step is also included in the FUGUE GUI option. There is only one problem which i would like to clarify with you, before that, i would like to mention that i followed exactly the same steps as mentioned in FSL's FUGUE course website where  i first converted my phase image to -pi to +pi range then applied PRELUDE to unwrap it, then converted to rad/sec and then fed the field map to pre stats part of FUGUE GUI and set the settings there as per your guidelines. My final result image filtered_func_data has intensities which range from 0 to 271021 whereas my original DTI image before field map correction has intensities from 0 to 2825 i understand that intensities will be modified in my fieldmap corrected image due to so many processing steps but my question is; is this high intensity value changes common after field map correction or am i making any mistake and will this high intensity values affect DTI parameters like FA, RA and other DTI metrics which i would like to calculate after this distortion correction step.
One other question is, in FUGUE GUI i didn't choose a value for FWHM explicitly as i fed values for dwell time and % signal threshold values, how is this FWHM value chosen whether the algorithm calculates the appropriate value by using some kind of iterative procedure.
If i have not given you enough information kindly inform me, i will get back to you with details.

Thanks a lot for your kind help. Wishing you a Very Happy New Year. I

Thanks

Regards
venkateswaran



-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
Sent: Tue 12/23/2008 5:48 PM
To: [log in to unmask]
Subject: Re: [FSL] Fugue -field map correction
 
Hi,

You are right about the units of dwell time - in the GUI they are in  
ms, so 0.85 should be OK.
What you are doing sounds generally right, although I would turn off  
spatial smoothing as well.
You don't need to specify a TR or a highpass filter cutoff for this  
application (you do need to
turn the filtering off on the pre-stats tab).

For signal loss you could go down to 0% for spin-echo EPI, but it  
won't really hurt
to have it at 10%.  You shouldn't need to do registration either.  So  
basically it all sounds
fine except for a bit of extra/unnecessary smoothing.  I would expect  
you to get reasonable
results and don't understand why you get excessively large  
intensities.  What other things
go wrong?  Does it apply too strong a change, or not enough, or the  
wrong direction, or what?

Are you also looking at the FEAT output report (the report.html page  
and the pre-stats output)?
This will help diagnose whether there is a problem in registration or  
field-map preparation or
direction of warping.  Look at the fsl course practical on FUGUE  
(under registration) for more help.
   http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/reg/index.html#fugue

If you still cannot figure out what is going wrong then let us know.
All the best,
	Mark



On 23 Dec 2008, at 21:06, Rajagopalan, Venkateswaran wrote:

> Dear Matt,
>
> Thanks,  i followed exactly the commands you described when i used  
> command line approach that is yours i divided my dwell time = 0.85  
> msec by 1000 as you showed, whereas in GUI mode i have to enter them  
> in msec only. Thanks for your kind infromation.
>
> Regards
> venkateswaran
>
> ________________________________
>
> From: FSL - FMRIB's Software Library on behalf of Matt Glasser
> Sent: Tue 12/23/2008 3:47 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Fugue -field map correction
>
>
>
> 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 <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 <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.
>



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

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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