Also, here is another place you can look, when Q's like this come up: https://wiki.humanconnectome.org/display/PublicData/HCP+Data+Release+Update s%3A+Known+Issues+and+Planned+fixes
-- 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 11/3/15 8:19 AM, "Donna Dierker" <do...@brainvis.wustl.edu> wrote: Hi Niklas, I found this note here: http://www.humanconnectome.org/documentation/ > IMPORTANT: Subjects 209733 and 528446 removed from ConnectomeDB. > > Second-level QC revealed two Q2 subjects, 209733 and 528446, with >structural brain abnormalities, specifically gray matter heterotopia, >that affect the functional and structural connectivity of these subjects. >All data from these subjects has been removed from ConnectomeDB and we >recommend that data from these subjects NOT be used in analyses. These >subjects were included in the Unrelated 40, Unrelated 80, and Related 120 >groups on ConnectomeDB and were part of Connectome in a Box distributions >until May 2014. Jenn can no longer say I never look at the documentation. ;-) Donna On Nov 3, 2015, at 3:51 AM, Niklas Kasenburg <niklas.kasenb...@di.ku.dk> wrote: > Hi Michael, > > thanks for the quick help. That indeed solved my problem! > > On another note a question to the whole HCP community: > > I realised that when choosing 40 subjects, there is only data > for 38. I have data from a previous release (Q3) that included > all 40 subjects. So I was wondering if there is any reason > that these two subjects (ID: 528446 and 209733) were removed. > > Best, > Niklas > > On 28/10/15 16:43, Harms, Michael wrote: >> >> Hi, >> If you download the "Structural Extended Preprocessed" package for each >>subject you want, you'll get the actual FS output files, in the FS >>output directory structure. >> >> 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: Niklas Kasenburg <niklas.kasenb...@di.ku.dk> >> Date: Wednesday, October 28, 2015 10:31 AM >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: [HCP-Users] Running TRACULA on the HCP data >> >> Dear HCP experts, >> >> I want to run TRACULA (included in Freesurfer) on a couple of subjects >>from the HCP data >> using the preprocessed diffusion data. However, to be able to run >>TRACULA you need to >> have run recon-all on the structural data of the same subject. Since >>the HCP data was >> processed with Freesurfer, I was wondering if I can avoid this step (to >>save time). >> >> So I tried to find out which files I need from the recon-all output, >>which are the following: >> >> $SUBJECTS_DIR/<subject_id>/mri >> ../orig.mgz >> ../brain.mgz >> ../aparc+aseg.mgz >> ../brainmask.mgz >> ../ribbon.mgz >> ../filled.mgz >> ../aseg.mgz >> >> $SUBJECTS_DIR/<subject_id>/surf >> ../{l,r}.white >> ../{l,r}.pial >> >> $SUBJECTS_DIR/<subject_id>/label >> ../{l,r}.aparc.annot >> >> The first five files in $SUBJECTS_DIR/<subject_id>/mri/ should be >>identical to the following >> files provided in the preprocessed structural HCP data and can be >>converted to .mgz with >> mri_convert : >> >> <subject_id>/T1w >> ../T1w_acpc_dc_restore.nii.gz >> ../T1w_acpc_dc_restore_brain.nii.gz >> ../aparc+aseg.nii.gz >> ../brainmask_fs.nii.gz >> ../ribbon.mgz >> >> However, I wasn't able to find an equivalent for file filled.mgz, >>aseg.mgz or files in /label. Furthermore, there are >> multiple surface files (in T1w/Native , MNINonLinear and >>MNINonLinear/Native) which are >> in .gii format. Which ones should I use and how do I convert them to be >>identical to the >> recon-all output. >> >> In summary, I would like to know if there are files provided in the HCP >>data that are >> identical to the files I need from recon-all and how to convert them to >>the correct >> format. >> >> Many thanks in advance and best regards, >> Niklas Kasenburg >> >> >> _______________________________________________ >> 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 > _______________________________________________ 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
