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]<mailto:[email protected]> | www.ki-su-arc.se<http://www.ki-su-arc.se/> ______________________________________ Karolinska Institutet – a medical university _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
