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
>>
>>
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> ===================================
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> P Please consider the environment before printing this e-mail
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> Cleveland Clinic is ranked one of the top hospitals
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> > for
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> locations.
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> Confidentiality Note: This message is intended for use
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> P Please consider the environment before printing this e-mail
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> 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.
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>
> 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
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> delivering the message to the intended recipient, you are
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