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Hi Carlos, Sorry this is a bit long! On 16/11/07 17:08, "Carlos Faraco" <[log in to unmask]> wrote: > I am sure some of these questions have been asked before, but the more I > read on the forum the more questions/problems/confusions arise. =] > > I will be running a DTI/fMRI study, DTI acq at 128X128 and fMRI at 64x64, > both non-spiral EPI, on a GE Signa 3T. We have presently been working on how > to acquire the proper GRE phase maps (yes, I know spin-echo is preferred, > but unfortunately we do not have time for such long scans) that will be in > the range of -pie to pie. The original phase maps we were acquiring had > values ranging *on average* from about 2800 to 6400 and we were not sure of > the conversion/scaling factors. > > A GE engineer suggested turning on parallel imaging, but then going into the > CV's and changing the acceleration factor to 1. This would not actually > acquire the images using parallel imaging, but would allow us to 1) bypass > the processing stream that was giving us the above values and 2) would then > give us values from -pie to pie x 1000. The only problem is that to do this, > we must use a Fast GRE sequence (acquire several lines of k-space per echo). > From reading other posts on the forum it seems this is not recommended; we > should only be using conventional GRE. Is this correct? The fast GRE sequences acquire a single line of k-space per echo, but you have less control over TR/TE than the standard GRE sequences. EPI gives distorted fieldmaps. You can aquire double-echo GRE to get both echoes needed to calculate the fieldmap, but you can have problems due to the two echoes being centred differently in the read-direction of k-space. This gives a linear ramp in the fieldmap that looks like a field gradient, but is actually a consequence of the Fourier shift theorem, so it's probably better to use two single-echo acquisitions > > If this is correct, do the images with values from 2800 to 6400 need to > scaled using fslmaths (I'm not even sure what scaling factor we would use) I don't think so. Without seeing your images, it's difficult to be sure, but three possibilities spring to mind to explain the values in your phase images. I'll list them with the least likely first. 1) You haven't set rhrcctrl correctly to output phase images. 2) Something I've seen in a few cases, when DICOM -> any other image format conversion software hasn't accounted for the possibility that DICOM image can contain variable number of bits per image, so one slice may only encode 11 bit, but the one next to it may encode 12. Similarly, negative numbers are not encoded converted correctly, and become high positive numbers, with the scaling depending on the number of bits encoded in the DICOM image. I doubt this is the case for you, as you would expect to see some numbers close to zero. You can check this by looking at the images on the scanner. Do they have values in the range -1000pi -> 1000pi. 3) Most likely, but will need a bit of explanation. You've acquired your field map images using a multi-channel receive coil, probably the 8-channel head coil. On GE scanners, when images from all the coils in the array are being combined (with ASSET off) it calculates the square root of the sum of squares for each coil. This even happens when you output real and imaginary parts. I tend to output real and imaginary so I'm not sure what happens to the phase, presumably it either calculates the square root of the sum of squares for each coil, or it calculates the phase from the already combined real & imaginary images. In either case this is invariably not what you want! There are two ways to get around the problem. i) on the scan interface change to the body coil for your fieldmap. ii) after you've hit download on the scan interface, but before scanning, change the CV saveinter to 1. You will then get the separate images from each coil, plus the coil-combined images. For example, if you want magnitude + phase using the 8-channel coil, you'll get a total of 18 [2x(8+1)] images per echo-time per slice. You can then calculate the (wrapped) fieldmap using the method described in Bernstein et al, Magn Reson Med 32, 330-334, 1994. The SNR in the field maps will be much better than using the body coil, with the only drawback being increased storage space, but then disc space is cheap. In both cases (i & ii) the phase images should be correctly scaled to -1000pi -> + 1000pi. Personally, I prefer to output the real & imaginary parts, then calculate the phase with the atan2 function. Hope that helps. Dave > or do the fugue or prelude programs look at the header info and scale > automatically since we will be using NIFTI format? I just read a post a > little while ago that mentioned FSL ingnoring the scalling factor in the > header for analyze, but not NIFTI files. > > Lastly, the GRE phase maps will be acquired at 128x128, is it ok to use > these to correct for the distortion in the fMRI 64x64s (even though there > probably will not be much)? Reason for using 64x64, instead of 128x128, is > to reduce slice thickness (3mm) and use the same for DTI then overlay. > > Thank you, > > Carlos