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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?
Loading volumesAfter which I left the -div0.00246 away.
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.
I think this is thelow thousands for a typical subject and scanner.
most likely cause for your problems. I'd normally expect
values inside the fieldmap image to be in the hundreds to
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!2008/7/30 Mark Jenkinson <[log in to unmask] <mailto:[log in to unmask]>>
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**
<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]>>>
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]>>>
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