Re: [HCP-Users] Fwd: Regarding: No FieldMap_Magnitude in lifespan dataset

[Glasser, Matthew]

In ${GitRepo}/Examples/Scripts/PreFreeSurferPipelineBatch.sh change these variables to use spin echo field maps to correct T1w and T2w scans for readout distortion in the HCP LifeSpan scans: AvgrdcSTRING="SiemensFieldMap" To AvgrdcSTRING=“TOPUP" MagnitudeInputName="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_FieldMap_Magnitude.nii.gz" To MagnitudeInputName=“NONE" PhaseInputName="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_FieldMap_Phase.nii.gz" To PhaseInputName=“NONE" TE=“2.46" To TE=“NONE" SpinEchoPhaseEncodeNegative="NONE" To SpinEchoPhaseEncodeNegative="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_LR.nii.gz" SpinEchoPhaseEncodePositive="NONE" To SpinEchoPhaseEncodePositive="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_RL.nii.gz" DwellTime="NONE" To DwellTime=“0.000580002668012” #From spin echo field map SEUnwarpDir="NONE" To SEUnwarpDir=“x” #For LR/RL spin echo field map TopupConfig="NONE" To TopupConfig=“${HCPPIPEDIR_Config}/b02b0.cnf”  Peace, Matt. P.S.  Tim, and Jenn, this info should probably be posted somewhere as I’m sure this won’t be the last question about this.   From: Dr Sampada Sinha <drsampadasi...@gmail.com> Date: Friday, February 6, 2015 at 11:07 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Fwd: Regarding: No FieldMap_Magnitude in lifespan dataset Many thanks Michael for your reply! Pardon me since I am new to the HCP analysis, you mentioned about using a pair of SpinEchoFieldMap scans for correction of T1 and T2w scans. Does that mean I make change to the PreFreeSurferPipelineBatch.sh (since thats my launch script here)? In the script in the MagnitudeInputName and PhaseInputName do I change it to NONE and in the SpinEchoFieldMaps do I change the script to  ${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_RL/LR.nii.gz?  What do I write in DwellTime?? Appreciate your help. Thanks and regards, Sampada _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users