Re: [HCP-Users] pipeline v2.0

[Harms, Michael]

Hi, See Jenn's earlier post, which I think addresses all this.  I'll repeat her comment that we already make available "level2" task data, so depending on your goals, it may not even be necessary for you to run the level1 and level2 task analysis yourself. 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: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Reply-To: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Date: Friday, August 8, 2014 10:55 AM To: "Harms, Michael" <mha...@wustl.edu>, "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: Re: [HCP-Users] pipeline v2.0 Dear MH Thank you so much for your time.I read Glasser et al and deduce that functional images are normalized and registered to both MNI space and their corresponding structural image.However,encountered"Registeration has not been run for all of the FEAT directoies that you have selected for group analysis,turn on and set up registeration"  in the FSL. As far as I understand by running "prepare_level2_feat_analysis.sh" I could  overcome this error,but it is not included in data directories. Do you know where I could download this file for Q1 motor task data?Do you have any other suggestions? many thanks, Mahsa On Friday, August 8, 2014 6:49 PM, "Harms, Michael" <mha...@wustl.edu> wrote: Hi Mahsa, Yes, the volume data is already in MNI space. When you posted on the SPM-list, I suggested that you review Glasser et al., 2014, and the HCP documentation, which together detail the processing steps performed.  Have you done that already?  If so, please provide more specific questions about what you don't understand about the pipeline. 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  63110Email: mha...@wustl.edu From: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Reply-To: Mahsa Alizade shalchy <ma.shal...@yahoo.com> Date: Friday, August 8, 2014 9:15 AM To: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: [HCP-Users] pipeline v2.0 Dear HCP users Hi I am working on HCP motor task data which is pre processed by: structural pipeline v2.0 functional pipeline v2.0 Does this mean the functional data is normalized and warped into  MNI space? could you please name the performed  steps in pipeline v2.0? many thanks, Mahsa   _______________________________________________ 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.   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