Re: [HCP-Users] Missing T1w_acpc_dc_restore files

[Harms, Michael]

Every subject that goes through the structural pipeline will have a T1w_acpc_dc_restore.nii.gz file.  Could you give some specific subject IDs for which that isn’t the case, so that our IT folks can look into what be going on with Amazon S3? 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: <hcp-users-boun...@humanconnectome.org> on behalf of Gregory Butron <gregorybut...@gmail.com> Date: Tuesday, January 12, 2016 at 7:57 AM To: "Glasser, Matthew" <glass...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Missing T1w_acpc_dc_restore files Hello Matt, thanks for getting back to me. I have not downloaded all the structural files yet. I downloaded all the available files for a few subjects to test our software, but after testing I discovered that not all subjects have the same files available. Then I perused the files on the amazon S3 server to decide what I need to download. Grabbing the whole freesurfer directory for each subject (the directory containing the T1.mgz file) will probably work for me, but I'd like to know what sort of pre-processing has been done to it. If every subject had a T1w_acpc_dc_restore.nii.gz file I would be all set, because the reference manual explains exactly what that file is and what preprocessing and transforms have been applied to it. But since some of the subjects (~25%) don't have this file available, I need to use something else. When I say I can't find a file, or that a subject doesn't have a file, I mean that I don't see it on the amazon s3 server. Thanks, Greg B. On Mon, Jan 11, 2016 at 6:31 PM, Glasser, Matthew <glass...@wustl.edu> wrote: Did you also download the structural packages for those subjects? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Gregory Butron <gregorybut...@gmail.com> Date: Monday, January 11, 2016 at 1:54 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Missing T1w_acpc_dc_restore files Hi All. I'm working with MEG data and I want to coregister it to the T1w_acpc_dc_restore.nii.gz processed structure scan as recommended by the reference manual. I downloaded the MEG data for the subjects who had resting state MEG data, but I discovered that 16 of them do not have a T1w_acpc_dc_restore.nii.gz file. Is there a reason why these subjects don't have this structure file? One of the subjects (725751) don't have any MRI data at all, so I suppose that is an excellent reason for not having the structure file, but I am a little confused by the others.  Since almost a quarter of the subjects with MEG data don't have the T1w_acpc_dc_restore.nii.gz file, I would like to use an alternative. Every subject that has a MRI scan has a T1.mgz file, so I think I can use this file instead, but I have a few questions that I have not found answers to in the documentation. First, what coordinate system does the T1.mgz file (i.e. s3://hcp-openaccess/HCP/subjectID/T1w/subjectID/mri/T1.mgz) use? I think I would relate it to the MEG data using the vox07mm transforms that come with the MEG data, but I haven't found confirmation of that in the documentation. Second, what sort of preprocessing has been done to the T1.mgz file? Have the axes been realigned? Has it been mapped to fit any standard models? Thank you for your time, Gregory Butron _______________________________________________ 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   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