Re: [HCP-Users] File 001.mgz

[Harms, Michael]

The 001.mgz is a file created "internal" to the FS processing.   I would use the T1w_acpc_dc_restore.nii file that you mentioned. 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: Gregory Butron <gregorybut...@gmail.com> Date: Monday, December 14, 2015 2:03 PM To: "Harms, Michael" <mha...@wustl.edu> Cc: Linda Larson-Prior <lin...@npg.wustl.edu>, Donna Dierker <do...@brainvis.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] File 001.mgz Hi all, thanks for the feedback. We are testing out some preprocessing software we wrote ourselves for some of our own MEG data collections. We wanted to see how our software works with the raw MEG data, and also attempt to co-register it to the MRI structural scans. We use the structural scans for localizing the MEG signals, and also for making a volume conduction model. Each subject also has the T1w_acpc_dc_restore.nii file, which might be more appropriate for what we are attempting to do. I was just curious about what the 001.mgz file was because it is in a format that our own software can already recognize and use. The file just isn't mentioned anywhere in the documentation (I haven't found it in the documentation, at any rate), so I just wanted to clarify what it was. On Mon, Dec 14, 2015 at 1:56 PM, Harms, Michael <mha...@wustl.edu> wrote: Right, so doesn't the MEG pipeline already provide what the user requested because users can't generate it themselves because properly registering the MEG to the T1 structural requires use of a non-defaced T1, and that isn't provided externally due to privacy considerations? -- 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 On 12/14/15 1:41 PM, "Larson-Prior, Linda" <lin...@npg.wustl.edu> wrote: The MEG data do not contain the original T1 images used to create the head models.  This file seems to belong to the MRI processing pipeline outputs as Donna suggested in her response ***********  NOTE NEW ADDRESS L.J. Larson-Prior, PhD University of Arkansas for Medical Sciences Department of Psychiatry 4301 W. Markham #554 Little Rock AR 72205 email: ljlarsonpr...@uams.edu ph: 501-526-8100 mobile: 314-303-3498 On 12/14/15, 1:33 PM, "hcp-users-boun...@humanconnectome.org on behalf of Harms, Michael" <hcp-users-boun...@humanconnectome.org on behalf of mha...@wustl.edu> wrote: > >Does the MEG specific processing not already contain what you need? > >-- >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 > > > > >On 12/14/15 11:40 AM, "Donna Dierker" <do...@brainvis.wustl.edu> wrote: > >I think this is just an output of the Freesurfer processing.  The stuff >here: > >> /MyDataPath/subjectID/T1w/subjectID > >Š is subjectID's freesurfer subject directory. > > >On Dec 14, 2015, at 11:38 AM, Gregory Butron <gregorybut...@gmail.com> >wrote: > >> Greetings! >> I am a Biomedical Engineering Graduate student who has recently begun >>doing research with MEG and EEG data. >> >> I've been exploring the HCP open access data, and there is a particular >>file that is not mentioned or explained in any of the documentation that >>I've searched. >> >> For each subject's data directory there we have a folder of the form: >> /MyDataPath/subjectID/T1w/subjectID/mri/orig/ >> and the orig folder has a file (usually) named 001.mgz >> >> I believe that this should just be a structural scan of the subject in >>the compressed mgh format. However, since the file is not mentioned in >>any of the documentation I've looked through, I want to make sure that >>001.mgz isn't a standard model or anything like that. >> >> The reason I'm interested is because we can use this to create some >>volume conduction models related to processing the raw MEG data. >> >> If anyone knows for sure what this file is, or can point me toward the >>documentation I should be looking at, I would really appreciate it. >> >>  - Greg B. >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > >_______________________________________________ >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. 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