Hi Gregory, Although it is not clear to me why you would need the anatomical image when processing the MEG data - the coregistration information is provided in the MEG anatomy packages - the anatomicals you refer to (T1w_acpc_dc_restore.nii.gz) are available from the subjects’ MEG_anatomy packages. That is, I just downloaded MEG_anatomy for subject 105923 and it seems to be there. Are you sure you have been looking in the right place?
Best wishes, Jan-Mathijs On Jan 12, 2016, at 3:59 PM, Gregory Butron <[email protected]> wrote: > Of course. The list below was generated by my python script, but I manually > checked a few of the subjects as well to confirm that it was giving a true > output. > > s3://hcp-openaccess/HCP/104012/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/105923/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/111514/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/146129/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/153732/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/156334/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/175540/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/192641/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/287248/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/512835/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/660951/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/662551/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/715950/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/725751/ does not have T1w folder > s3://hcp-openaccess/HCP/783462/ does not have T1w_acpc_dc_restore.nii.gz > s3://hcp-openaccess/HCP/825048/ does not have T1w_acpc_dc_restore.nii.gz > > This script only looked for the T1w_stuff_stuff.nii.gz file on subjects that > had resting state MEG data. I can check all the subjects if you like, but > below is a list of the subjects that the script checked for the > T1w_stuff.nii.gz file in. > > Searched subjets: > 100307/ > 102816/ > 104012/ > 105923/ > 106521/ > 108323/ > 109123/ > 111514/ > 113922/ > 116524/ > 125525/ > 133019/ > 140117/ > 146129/ > 149741/ > 151526/ > 153732/ > 156334/ > 158136/ > 162026/ > 166438/ > 172029/ > 175540/ > 177746/ > 181232/ > 182840/ > 185442/ > 187547/ > 189349/ > 191033/ > 191437/ > 191841/ > 192641/ > 195041/ > 200109/ > 204521/ > 205119/ > 212318/ > 221319/ > 233326/ > 250427/ > 255639/ > 287248/ > 293748/ > 352132/ > 352738/ > 433839/ > 500222/ > 512835/ > 559053/ > 568963/ > 599671/ > 601127/ > 660951/ > 662551/ > 665254/ > 680957/ > 715950/ > 725751/ > 783462/ > 814649/ > 825048/ > 872764/ > 877168/ > 898176/ > 912447/ > 917255/ > > > > On Tue, Jan 12, 2016 at 8:49 AM, Harms, Michael <[email protected]> wrote: > > 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: [email protected] > > From: <[email protected]> on behalf of Gregory Butron > <[email protected]> > Date: Tuesday, January 12, 2016 at 7:57 AM > To: "Glasser, Matthew" <[email protected]> > Cc: "[email protected]" <[email protected]> > 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 <[email protected]> wrote: > Did you also download the structural packages for those subjects? > > Peace, > > Matt. > > From: <[email protected]> on behalf of Gregory Butron > <[email protected]> > Date: Monday, January 11, 2016 at 1:54 PM > To: "[email protected]" <[email protected]> > 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 > [email protected] > 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. 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