Dear Matt, You mentioned <1) Are these from a Siemens scanner? If so, the procedure looks correct, though I would check the original phase image range to see if how it is scaled. If it is scaled from 0 to 4095, then what you have is correct. If it is scaled from -4096 to 4096, then you need to subtract 4096 and divide by 4096. > Why is it correct? I don't know why substract 4096 and divide by 4096 when image from siemens scanner is scaled from -4096 to 4096. cheers, dongha [log in to unmask] 쓴 글: > > Dear Matt, > > I see. I've had some problems unwarping a set of partial volume EPI > images. Initially, i thought it might have been due to the > orientation. If that's the case, i guess the difference in number of > slices between the fieldmaps (which have 46 slices) and the EPI that > i'm trying to correct (which has 26 slices) could possibly cause a > problem during the registration of the fieldmap magnitude to the EPI? > > I've read somewhere on the fsl website about registering the partial > FOV to a full brain EPI.. Would that help? > > cheers, > ying > > > > > *"Matt Glasser" <[log in to unmask]>* > Sent by: "FSL - FMRIB's Software Library" <[log in to unmask]> > > 09-Nov-2009 16:19 > Please respond to "FSL - FMRIB's Software Library" <[log in to unmask]> > > > > To > [log in to unmask] > cc > > Subject > Re: [FSL] EPI Distortion Correction Queries... > > > > > > > > > > No that should not matter, as the magnitude of the field map will be > registered to the fMRI. However, the field map should include the > whole fMRI volume in its FOV or the parts outside will not be corrected. > > Peace, > > Matt. > > ------------------------------------------------------------------------ > > *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *[log in to unmask]* > Sent:* Monday, November 09, 2009 9:08 AM* > To:* [log in to unmask]* > Subject:* Re: [FSL] EPI Distortion Correction Queries... > > > Dear Matt, > > Thank you very much for your reply.. > > Do you think it would be a problem if the EPI image is not in the same > orientation (as in if you look at the sagittal plane, it's not tilted > the same way) as the gradient fieldmaps? > > cheers, > ying > > *"Matt Glasser" <[log in to unmask]>* > Sent by: "FSL - FMRIB's Software Library" <[log in to unmask]> > > 22-Oct-2009 16:38 > > > Please respond to "FSL - FMRIB's Software Library" <[log in to unmask]> > > > > > > To > [log in to unmask] > cc > > Subject > Re: [FSL] EPI Distortion Correction Queries... > > > > > > > > > > > 1) Are these from a Siemens scanner? If so, the procedure looks > correct, though I would check the original phase image range to see if > how it is scaled. If it is scaled from 0 to 4095, then what you have > is correct. If it is scaled from -4096 to 4096, then you need to > subtract 4096 and divide by 4096. > > 2) That sounds like a good way of determining whether the unwarp > direction is y or y-. You can try registering the images to an > undistorted anatomical image to more clearly see which one is > correcting the distortion and which one is making it twice as bad. > > 3) I would do the MCFLIRT and then compare vs the undistorted structural > > Peace, > > Matt. > > > > ------------------------------------------------------------------------ > > * > From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *[log in to unmask]* > Sent:* Thursday, October 22, 2009 6:19 AM* > To:* [log in to unmask]* > Subject:* [FSL] EPI Distortion Correction Queries... > > > Dear Sir/Madam, > > I have been trying to work with EPI Distortion correction in > accordance to the documentation as follows: > http://www.fmrib.ox.ac.uk/fsl/fugue/index.html, > http://www.fmrib.ox.ac.uk/fslcourse/ (lecture and practical). However, > i am unsure if i've understood them correctly, and was hoping you > would be kind enough to provide me with some advice. > > 1) i'll have two magnitude images (one from each TE, 5ms vs 8ms) and > one phase difference image from the scanners. And i would prepare them > as follows: > > # to bet the magnitude image > standard_space_roi {mag_5ms} premask -b > bet2 premask mag_brain -f 0.4 > > # to convert phase image to radians/s > fslmaths {phase_diff} -sub 2048 -div 2048 -mul 3.14159 rad_phase -odt > float > prelude -p rad_phase -a mag_brain -o urad_phase > fslmaths urad_phase -div 0.00246 urads_phase > > 2) then within FEAT, using the B0 unwarping option alone, i'd input > mag_brain as the magnitude image, and urads_phase as the phase image, > and try both y and -y to figure out which direction is better. > > 3) According to our physicist, the direction of distortion should be > posterior towards anterior. In order to figure out whether the unwarp > was an improvement: > > - i would compare examplefunc vs example_func_orig_distorted and see > which regions (with special attention to frontal, inferior temporal > regions) to see whether they were shifted more anteriorly with unwarping > - i would look at the example_func2highres vs > example_func_orig_distorted2highres to see which has a better > registration with the highres (this is especially challenging as i can > only judge using the ventricles as the cortical areas are difficult to > judge) > > > My queries would be: > 1) Does the preparation of the gradient echo images sound correct? > 2) Do the methods of deducing whether there was an improvement make > sense? If not, are there other ways of doing so, such as judging from > the feat report EPI correction section? > 3) Would it make sense to do a comparison by (a) applying unwarp to > the EPI alone, or (b) with the rest of the preprocessing e.g MCFLIRT > etc, (c) within subject, or across subject (on a group level) to be > able to judge if unwarp has caused an improvement? > > > Your help would be immensely appreciated. Looking forward to hear from > you. > > Yours faithfully, > Ying > ----------------------------------------------------------- > This e-mail was sent by GlaxoSmithKline Services Unlimited > (registered in England and Wales No. 1047315), which is a > member of the GlaxoSmithKline group of companies. The > registered address of GlaxoSmithKline Services Unlimited > is 980 Great West Road, Brentford, Middlesex TW8 9GS. > ----------------------------------------------------------- > ----------------------------------------------------------- > This e-mail was sent by GlaxoSmithKline Services Unlimited > (registered in England and Wales No. 1047315), which is a > member of the GlaxoSmithKline group of companies. The > registered address of GlaxoSmithKline Services Unlimited > is 980 Great West Road, Brentford, Middlesex TW8 9GS. > ----------------------------------------------------------- > ----------------------------------------------------------- > This e-mail was sent by GlaxoSmithKline Services Unlimited > (registered in England and Wales No. 1047315), which is a > member of the GlaxoSmithKline group of companies. The > registered address of GlaxoSmithKline Services Unlimited > is 980 Great West Road, Brentford, Middlesex TW8 9GS. > ----------------------------------------------------------- >