Dear Markus,
The input to PRELUDE needs to be in radians - that is, a range of 2*pi,
so -3.14 to +3.14 is good. The input to FEAT needs to be a fieldmap in
radians *per second* or rad/s or more concisely, but maybe confusingly,
rads. Hence you should not divide by 0.00246 before unwrapping with
prelude, but you should divide the *output* of prelude by this to convert
it to radians per second.
The range I was talking about (hundreds to low thousands) is for the
input to FEAT - that is, the fieldmap in radians per second.
I hope this is clear.
All the best,
Mark
Markus Gschwind wrote:
> Hi Mark!
>
> Thanks a lot again!
>
> but the fieldmap image is not in rad/s. The values inside the
> brain are really quite small. Did you remember to convert
> your input into radians and then divide by the difference of
> echo times for your fieldmap acquisition?
>
>
> Yes, I think, I did.
> As you already saw, I calculated:
>
> * fslmaths FMphase.nii.gz -mul 3.14159 -div 4096
> FMphase_rad.nii.gz -odt float
>
> * prelude -u unwarped_phase -a FMmag1_rad.nii.gz -p
> FMphase_rad.nii.gz -v
>
> That is to say: Initially I used wrongly
>
> * fslmaths FMphase.nii.gz -mul 3.14159 -div 4096 -div 000246
> FMphase_rad.nii.gz -odt float
>
> which you supposed to be correctly *-div 0.00246* (2.46 ms beeing the
> difference of TEs)
>
> However, that one gave me the following error (using the lines above):
>
> Loading volumes
> Phase loaded
> Magnitude loaded
> ERROR: input phase image exceeds allowable phase range.
> Allowable range is 6.283 radians. Image range is: 2552.89 radians.
> Aborting.
>
> After which I left the -div0.00246 away.
>
>
> I think this is the
> most likely cause for your problems. I'd normally expect
> values inside the fieldmap image to be in the hundreds to
>
> low thousands for a typical subject and scanner.
>
> Do you mean the valuees inside the unscaled or the scaled fieldmap?
>
> In fslview the histogram of the unwarped_phase, which I entered in
> FEAT, gives me values between -3.14 and +3.14 (the values of the
> original_phase are 0 to 4096)
>
> I thus -add pi to the rescaling above and rerun the whole thing
>
> * fslmaths FMphase.nii.gz -mul 3.14159 -div 4096 -add 3.14159
> FMphase_rad.nii.gz -odt float
>
> and now the range of the unwarped_phase is 0 to 6.28.
>
> However, after doing the FEAT pre-processing the "unwarping shift map,
> in voxels" indicates still -0 to +0 and there is still nothing being
> unwarped!
>
> It seems that I don't understand...
>
> Desperate, but very gratefull,
> Markus
>
>
>
>
>
>
>
>
>
>
>
>
> 2008/7/31 Mark Jenkinson <[log in to unmask]
> <mailto:[log in to unmask]>>
>
> Hi,
>
> You are quite right - nothing is being done.
> You can easily see this by looking at the third image
> in the pre-stats (Unwarping shift map, in voxels) which
> indicates that the range of shift is -0.0 to +0.0 - that is,
> nothing at all.
>
> This is usually due to either the echo time or echo spacing
> being incorrect or the fieldmap image not being in rad/s.
> From your log I can see that the TE and echo spacing are OK,
> but the fieldmap image is not in rad/s. The values inside the
> brain are really quite small. Did you remember to convert
> your input into radians and then divide by the difference of
> echo times for your fieldmap acquisition? I think this is the
> most likely cause for your problems. I'd normally expect
> values inside the fieldmap image to be in the hundreds to
> low thousands for a typical subject and scanner.
>
>
> All the best,
> Mark
>
>
>
> Markus Gschwind wrote:
>
> Hi Mark!
>
> What a service! Thanks a lot!
>
> And the patch worked! (That means it shows good images in the
> report and it did something).
>
> However, I am still not sure if there has been a real unwarping:
> When I compaire example_func.nii.gz and
> example_func_orig_distorted.ii.gz (in fslview and by fslmaths
> -sub or -mul), it seems that the only thing that happened was
> *bet*!
>
> Please, could you have a last look? I am very gratefull!
> The # is 540650.
>
> Thank you so much!
> Markus**
>
>
> 2008/7/30 Mark Jenkinson <[log in to unmask]
> <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>>
>
>
> Hi Markus,
>
> There are several things here.
>
> One is that there is two bugs in feat which are problematic
> for you.
>
> The first we've seen before - which is just that the
> reported images
> on the webpage are wrong when the voxel size for the
> fieldmap and
> epi are different, even though all the images as viewed in
> fslview are
> absolutely fine. This is something which didn't quite make
> the last
> patch, but will be in the next FSL release coming very shortly.
>
> The second bug is something I hadn't seen before which is a
> failure
> to make one transformation matrix when using fieldmaps *and* an
> initial_highres image. However, in your case I don't quite
> understand
> why you are using the same image for highres and
> initial_highres, so
> I would say that you should not put in an initial_highres here.
>
> The other thing is that you do not need to convert your
> magnitude
> images to radians - only the phase image needs to be converted.
> That is, only the first fslmaths line that you included is
> necessary,
> although there is probably little danger in what you'd done
> with the
> magnitude images.
>
> I've made a patched version of the featlib.tcl file which
> should fix
> both the bugs. You can download this file from:
>
> http://www.fmrib.ox.ac.uk/fsldownloads/patches/featlib.tcl Once
> you have the file, put it in $FSLDIR/tcl/ and try
> re-running again,
> without using the initial_highres, and hopefully it will work
> correctly.
>
>
> All the best,
> Mark
>
>
>
> Markus Gschwind wrote:
>
> Hi Mark!
>
> Here comes the result of what I did after your
> recommandations
> from below.
>
> i.e., I did:
>
> fslmaths FMphase.nii.gz -mul 3.14159 -div 4096
> FMphase_rad.nii.gz -odt float
> fslmaths FMmag1.nii.gz -mul 3.14159 -div 4096
> FMmag1_rad.nii.gz -odt float
> fslmaths FMmag2.nii.gz -mul 3.14159 -div 4096
> FMmag2_rad.nii.gz -odt float
>
> prelude -u unwarped_phase -a FMmag1_rad.nii.gz -p
> FMphase_rad.nii.gz -v
>
> However I am not sure that this was correct:
> 1. Concerning the *Thresholded signal loss weighting
> image*:
> Why is it red in the upper half? It seems that the EPI
> (=yellow box) is only about half the size of the
> fieldmap and
> that it has not been registered.
>
> 2. Concerning the *Unwarping shift map, in voxels* : I
> think
> that it confirms my belief, the EPI and fieldmap have
> not been
> registered.
>
> I uploaded the unwarp directory of my .ica folder and the
> report.html.
> The # is 807456.
>
> I would be very glad if you could have a look!
>
> Thanks in advance and all the best!
> Markus**
>
>
> 2008/7/24 Mark Jenkinson <[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>
>
>
> Hi,
>
> You do not need to worry about the EPI and fieldmap
> being
> different
> sizes, resolutions or orientations (as long as the
> orientation
> difference
> is small) as the FEAT GUI will take care of all of
> that by
> doing
> appropriate
> registration steps. Hence it is not necessary to do the
> registrations
> yourself, and the FEAT GUI applies several more
> complicated
> steps
> internally which should improve the results compared
> to a
> single
> registration.
>
> The scaling looks fine except that -div 00246 should
> assumedly be
> -div 0.00246 or similar.
>
> I've had a look at the files, but unfortunately
> cannot see
> any images
> as you only sent the .html files. However, in the
> log it
> is clear
> that
> something has gone wrong and that it cannot
> generate/find some
> files. Check that all of your input images are
> correctly
> specified
> and that the images themselves are good (look at
> them with
> FSLView).
>
> If you still cannot work out what is wrong (and redo
> things
> without
> the initial manual registration steps that you've been
> doing) then
> contact us again.
>
> All the best,
> Mark
>
>
> Markus Gschwind wrote:
>
> Dear fieldmap experts!
>
> I am getting data from another MRI site (Siemens
> Trio)
> with a
> fieldmap that has not the dimensions of the EPI
> data,
> thus I
> have to play around to make it work.
>
> I registered the magnitude1 to the EPI data (flirt),
> and then
> applied the .mat to the phase and magnitude2.
>
> I then rescaled the phase to radiant/s
> > fslmaths rFMphase.nii.gz -mul 3.14159 -div
> 4096 -div
> 00246
> rFMphase_rad.nii.gz -odt float
>
> and used prelude to unwarp the phase:
> > prelude -u unwarped_phase -a rFMmag1_rad.nii.gz -p
> rFMphase_rad.nii.gz -v
>
> At the end, I entered the registered magnitude1
> and the
> unwarped phase into the Melodic gui (echo
> spacing 0.58, ET
> 27ms, unwarp direction -y, signal loss threshold
> 10%)
>
> I wonder if everything is all right with what I
> did and I'd
> like to ask someone to have a look at the
> results, please.
> I uploaded (# *131961) *the pre-stats report and the
> log report.
>
> Thanks a lot to all your help!
>
> Markus
>
>
> -- Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>>>
> http://labnic.unige.ch
>
>
>
>
> -- Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>>
> http://labnic.unige.ch
>
>
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> <mailto:[log in to unmask]>
> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> http://labnic.unige.ch
>
>
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> <mailto:[log in to unmask]>
> http://labnic.unige.ch
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