Re: [HCP-Users] Clarifying the use of "scout" in the preprocessing scripts

[Harms, Michael]

Hi Craig, In our usage, the "scout" is indeed the SBRef for a given fMRI scan (although the pipelines are set up such that you can use other "scouts"). What we call "SpinEchoFieldMap_{RL,LR}" during scan collection are not field maps per se, but rather the actual reversed-PE, SE EPIs themselves (from which the field map is derived via 'topup'). Yes, pre-processing has to be done separately for each run.  Have you seen Examples/GenericfMRIVolumeProcessingPipelineBatch.sh?  If you take a look at that, I think that may clear up how you can run the processing for a number of scans, and it shows exactly what files are provided as inputs to the various arguments of GenericfMRIVolumeProcessingPipeline.sh 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: Craig Anthony Moodie <cmoo...@stanford.edu> Date: Tuesday, November 10, 2015 11:13 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Clarifying the use of "scout" in the preprocessing scripts Hello, I'm trying to implement a variant of the HCP style preprocessing using Nipype and I wanted to make sure I'm following the right steps.  From reading the scripts, the preprocessing paper, and the responses I could find on the mailing list it seems like you sometimes refer to the SBRef (or some mean/median volume) as the "scout" in the scripts. For instance, this seems to be the case for the TopupPreprocessingAll.sh script. However, for the distortion correction and fmri volume processing scripts, the scout is labelled as a pre-sat EPI input. Hence, I wanted to confirm that this input image is one of the gradient echo EPI scans from the reversed PE pair (e.g. one of a reversed PE pair of resting-state scans). In addition, it seems like the TopupPreprocessingAll.sh script is set up to use a pair of full, reversed-PE, SE EPI functional scans, but you are using the pair of SE fieldmaps instead when applying the ${SPIN_ECHO_METHOD_OPT} in the DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh script. Are these interpretations correct? And if so, would one run the GenericfMRIVolumeProcessingPipeline.sh script separately for each of a pair of PE reversed resting scans, or is there a way that both scans get processed at the same time that I missed. Thank you in advance for your help! Best, Craig. -- Craig Moodie Postdoctoral Fellow Poldrack Lab Department of Psychology Stanford University. _______________________________________________ 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