That looks good regarding setting up a standard field map. I would recommend setting the SBRef if it is available. I would recommend not smoothing the data more than the voxel resolution (can always do more later if you have to). I would recommend using MSMSulc instead of FS as MSMSulc produces better functional alignment and less distortion relative to FreeSurfer. You can get the MSM binary here: https://github.com/ecr05/MSM_HOCR/releases
In general we prefer the spin echo field maps because you can use them for bias correction too and some of the internal registrations are better conditioned, but regular field maps produce acceptable distortion correction. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of zhou y <[email protected]<mailto:[email protected]>> Date: Tuesday, June 5, 2018 at 11:48 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Applying field map from a double-echo gradient echo sequence to the GeneralfMRI Processing Pipeline Dear Sir/Madam, I am applying our lab's local 3T MRI data to the hcp minimal preprocessing pipelines. Since we used a field map from a double-echo gradient echo sequence different from HCP data which used the opposite phase encoded EPIs, I would like to check whether I have set the following parameters approriately with gradient distortion correction and later processing. UnwarpDir=`echo $PhaseEncodinglist | cut -d " " -f $i` fMRITimeSeries="${StudyFolder}/${Subject}/unprocessed/3T/${fMRIName}/${Subject}_3T_${fMRIName}.nii.gz" fMRISBRef="NONE" DwellTime="0.00049" # EchoSpacing="0.00049" DistortionCorrection="SiemensFieldMap" # we used Siemens for scanning BiasCorrection="NONE" SpinEchoPhaseEncodeNegative="NONE" # using regular FIELDMAP SpinEchoPhaseEncodePositive="NONE" #using regular FIELDMAP MagnitudeInputName="${StudyFolder}/${Subject}/unprocessed/3T/${fMRIName}/${Subject}_3T_FieldMap_merg.nii.gz" # 4D Magnitude volume with two 3D timepoints, we merged the fieldmap_long and fieldmap_short into one 4D file PhaseInputName="${StudyFolder}/${Subject}/unprocessed/3T/${fMRIName}/${Subject}_3T_FieldMap_phase.nii.gz" # using fieldmap_phase file GEB0InputName="NONE" DeltaTE="2.46" FinalFMRIResolution="2" # GradientDistortionCoeffs="${HCPPIPEDIR_Config}/coeff_SC72C_Skyra.grad" GradientDistortionCoeffs="/home/Projects/HCP_MINPre/Pipelines/global/config/coeff.grad" #from the scanning center with Siemens TopUpConfig="NONE" #using regular FIELDMAP TopUpConfig="NONE" #using regular FIELDMAP MCType="MCFLIRT" ----------------------------------------------------- LowResMesh="32" FinalfMRIResolution="2" SmoothingFWHM="4" GrayordinatesResolution="2" # RegName="MSMSulc" #MSMSulc is recommended, if binary is not available use FS (FreeSurfer) RegName="FS" ----------------------------------------------------- Actually I have tested some subjects to run these pipelines without any error reported. Yet I am still not sure whether I have set every parameter right or not. And how do I check the results? Best, Zoey _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
