 |
 |
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]> > 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] >> >> >> >> >> 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]>>> >> >> >> 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 >> > -- 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] http://labnic.unige.ch