Hi! Which GE scanner do you have? In the current version of the pipelines they included some code that I wrote to handle the B0 fieldmaps that our GE MR750 creates, which consists of a single image with 2 volumes: 1) the real fieldmap in degrees and 2) a magnitude image. Per the FUGUE guide (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide) the GeneralElectricFieldMapPreprocessingAll.sh script just converts the degree image to rads and masks the Magnitude image. Since the guide didn't ask for a demeaned magnitude image I didn't include that step, and its been working well for us. If your scanner can only give you complex/imaginary images, then the script I've written won't work unfortunately.
__________________________ gaurav patel [email protected] www.neurofreak.net On Mar 31, 2015, at 5:35 AM, Benjamin Garzon wrote: > > Dear all, > > I'm trying to use the Pipeline v.3.6.0 pre-release to run it on General > Electric 32-ch coil data. > > I am not sure that I am doing the right preprocessing steps to convert the > data I get from the scanner into the format expected by the pipeline. I would > be grateful if someone could confirm that what I am doing is right, or > alternatively indicate which are the correct steps. > > The data I got consists of real and imaginary images for 2 echo times, with a > TE difference of 2 ms. These are the steps I am following: > > 1 ) Generate a complex 4D image with two volumes corresponding to the 2 TEs > (using fslcomplex). > 2 ) Compute the magnitude image for the first echo (MAGNITUDE.nii.gz). > 3 ) Divide the second complex image by the first one to obtain a complex > image with phase equal to the phase difference between echoes > (ECHO_RATIO.nii.gz). > 4 ) Run prelude on ECHO_RATIO.nii.gz, which returns an unwrapped phase > difference image (PHASE_DIFF.nii.gz). This step may not be needed, as I > cannot see any wraps in ECHO_RATIO.nii.gz, but perhaps for other datasets > this will not be the case. > 5 ) Multiply PHASE_DIFF.nii.gz by -1000/(6.28*2) to obtain the fieldmap > (FIELDMAP.nii.gz). The factor 2 corresponds to the 2 ms TE difference, the > factor 1000 to the conversion to seconds, and the minus sign to ensure that > the high intensities in the fieldmap correspond to areas of strong > susceptibility, like for SIEMENS fieldmaps. If I am not wrong, this is needed > because of different handedness in GE and SIEMENS systems. > 6 ) Demean the fieldmap. I have noticed in the SIEMENS fieldmap preprocessing > SiemensFieldMapPreprocessingAll.sh, fsl_prepare_fieldmap has a demeaning step > which I cannot see it is done in GeneralElectricFieldMapPreprocessingAll.sh, > so I am including this before handing the fieldmap over to the pipeline. Not > sure I should do this, though. > 7 ) Merge the result in one 4D image, with the demeaned fieldmap as the first > volume and the magnitude image as the second one. > > Which is the magnitude of the shift that I should expect? I am looking at the > shift map obtained from one of the HCP subjects and the max values are around > .1, whereas for the General Electric data the max is around 6 times larger. > Is such a big difference possible between scanners or this means I am missing > something ? > > The sample spacing I am using is 0.000016, corresponding to the inverse of > the product of the dicom fields (0018,0095) and (0028,0010), as indicated in > PreFreesurferPipelineBatch.sh > > Any help or clarification is greatly appreciated! > Best regards, > > > Benjamín Garzón, PhD > Department of Neurobiology, Care Sciences and Society > Aging Research Center | 113 30 Stockholm | Gävlegatan 16 > [email protected] | www.ki-su-arc.se > ______________________________________ > Karolinska Institutet – a medical university > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
