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]>>
> 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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