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. 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 > > > ------------------------------ > > 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
