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. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
