Hi, I took a very quick look to see what direction this is heading. One initlal thing I noticed -- the files in $SUBJID/T1w are not in MNI152 space.
Cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of Psychiatry 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: <hcp-users-boun...@humanconnectome.org> on behalf of "Glasser, Matthew" <glass...@wustl.edu> Date: Tuesday, July 24, 2018 at 10:23 AM To: "Theis, Nicholas" <the...@upmc.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP pipeline working directory documentation I am not aware of such a document. I am happy to review it when you are ready for accuracy. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Theis, Nicholas" <the...@upmc.edu<mailto:the...@upmc.edu>> Date: Tuesday, July 24, 2018 at 9:54 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP pipeline working directory documentation Dear HCP creators and users- To better understand the HCP pipelines we have been documenting its output files. We want to identify the specific files produced by each stage of the pipeline (PreFreeSurfer, FreeSurfer, etc), and label what MRI preprocessing step the files represent (skull stripping, readout distortion correction, etc). To your knowledge, has anyone already created a similar document? We are hoping to make this list as complete -and helpful - as possible - although it is still a work in progress, and some aspects of it reflect our particular set-up. Feel free to view the document in the link below. https://docs.google.com/spreadsheets/d/16mKW14FvQr_Im57eVvhePeT-yuRl7IiaOfP7eDEfppE/edit?usp=sharing If this is something the wider community would find useful then we are happy to share it by other means, especially as it is completed. Any suggestions or corrections are welcomed. Best, Nick Theis [Image removed by sender.]<https://docs.google.com/spreadsheets/d/16mKW14FvQr_Im57eVvhePeT-yuRl7IiaOfP7eDEfppE/edit?usp=sharing> HCP_filenames_corresponding_processing_step<https://docs.google.com/spreadsheets/d/16mKW14FvQr_Im57eVvhePeT-yuRl7IiaOfP7eDEfppE/edit?usp=sharing> docs.google.com HCPstages Pipeline Stage, Location, Output File or Directory, Description, Links to References where applicable PreFreeSurfer,/ data2/ MRI/ Maria_K01/ HCPproc/${ SUBID}/ T1w, BiasField_acpc_dc, Bias Field( gradual intensity change across field of view) is corrected for using equation( 1) of Gl... _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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 ________________________________ 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
