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

[Harms, Michael]

Hi, Which version of the pipeline scripts are you working off?  I would suggest that you try referencing the latest "pre-release" version available at https://github.com/Washington-University/Pipelines/releases/ which appears to contain a good number of embedded comments in its PreFreeSurferPipelineBatch.sh to help you out. In particular, you will want to use "TOPUP" as your method for readout distortion correction, and a formula is provided for how DwellTime (really EchoSpacing) can be derived for Siemen's scanners. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: Dr Sampada Sinha <drsampadasi...@gmail.com> Date: Friday, February 6, 2015 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